PLEASE HELP I DON"T KNOW WHAT TO DO

Okay, so you need to get in touch with them right away and tell them they forgot the door on the coop - especially if it was advertised that way when you bought it. My recommendation would be to move the water outside into the run for sure, so it doesn't make a mess inside the coop, and put the feeder in a garage/shed/mud room/somewhere mice are excluded for the night - I realize that may not be a possibility for tonight, just saying for future, I put my feed away every night to try and limit the number of rodents I attract with it, whether you keep it inside the coop or in the run - mine is in the runs, but whichever you opt for should be fine. But you have to have the door on the coop. If some predator breaches the run, nothing stops it from getting into the coop.
There's one door on the side of the coop for human access, and then the hole that leads into the run for chicken access. I want both the feeder and the waterer in the run. I'm afraid that right now moving the food in and out every night is not an option-we should have secured our yard better. Apparently these hens fly???? Well??? In my experience they will flap up a few inches, a foot high at most. I'm worried that I'll have to literally construct an aviary type enclosure so that they can't get out. I'll draw up a quick thing so you can see better what's going on with it, and hopefully I'll get real pictures tomorrow. The run has fully enclosed hardware cloth, so no tunneling. There aren't any loose dogs in our area that would be at it. No coyotes or woods around my house, and there are fences on two sides of the backyard, so stuff doesn't move through too often. I have grit and shell containers that I was going to hang up for them in the run. I know I need them but I have NO IDEA how I'll get in to hang them. I was GOING to set everything up BEFORE putting in the chickens in the coop, but due to my lack of self confidence, I didn't say anything.
 
current setup.jpg

Here's a VERY messy, sketchy thing of the current setup. There is one big door into the coop, and one big door at the end of the run. That hole in the coop is where the chickens go through to get between coop and run. The weird blob in the run is the dust bath. The feeder and waterer are in the coop. There are no other doors than what you can see, and the nest boxes are internal. I did put a roof on the run-plywood with plastic sheeting, propped up on one end to let water run off and downhill. In the drawing it looks like it's on an angle, but it's on a flat surface.
 
There's one door on the side of the coop for human access, and then the hole that leads into the run for chicken access. I want both the feeder and the waterer in the run. I'm afraid that right now moving the food in and out every night is not an option-we should have secured our yard better. Apparently these hens fly???? Well??? In my experience they will flap up a few inches, a foot high at most. I'm worried that I'll have to literally construct an aviary type enclosure so that they can't get out. I'll draw up a quick thing so you can see better what's going on with it, and hopefully I'll get real pictures tomorrow. The run has fully enclosed hardware cloth, so no tunneling. There aren't any loose dogs in our area that would be at it. No coyotes or woods around my house, and there are fences on two sides of the backyard, so stuff doesn't move through too often. I have grit and shell containers that I was going to hang up for them in the run. I know I need them but I have NO IDEA how I'll get in to hang them. I was GOING to set everything up BEFORE putting in the chickens in the coop, but due to my lack of self confidence, I didn't say anything.

i started with adult chickens. We are 3 months on with RIR and Leghorns also, and I ran into similar issues.
Thing 1: they will calm down. Give them time.
Thing 2: chickens fly. Some better than others. I about peed myself when my leghorns got out and were running amuck. You can deter it by running some cording across the top of your run and this will help with predators.
Thing 4: leghorns are super skittish. Annoyingly so. That won’t change, it’s the breed.
Thing 5: it isn’t going to ever go the way you want it to. They’re animals and each have their own personality. Accept it now, and you’ll be calmer in the end. I currently have three coops because of unforeseen issues. Fun, no, but we have settled into a routine and things are going well, for the moment.
Last thing: you can likely fix your coop to your needs. I’ve made several adjustments from what I thought would work to what works better. My initial set up requires me to walk in for egg collection, which doesn’t bother me. I open their door, they come out to eat, and then I walk in. It isn’t the end of the world. You can make adjustments, and as long as you can keep them safe, take the minor inconveniences in stride, let them settle, then fix you’re troubles. It will be ok.
 
i started with adult chickens. We are 3 months on with RIR and Leghorns also, and I ran into similar issues.
Thing 1: they will calm down. Give them time.
Thing 2: chickens fly. Some better than others. I about peed myself when my leghorns got out and were running amuck. You can deter it by running some cording across the top of your run and this will help with predators.
Thing 4: leghorns are super skittish. Annoyingly so. That won’t change, it’s the breed.
Thing 5: it isn’t going to ever go the way you want it to. They’re animals and each have their own personality. Accept it now, and you’ll be calmer in the end. I currently have three coops because of unforeseen issues. Fun, no, but we have settled into a routine and things are going well, for the moment.
Last thing: you can likely fix your coop to your needs. I’ve made several adjustments from what I thought would work to what works better. My initial set up requires me to walk in for egg collection, which doesn’t bother me. I open their door, they come out to eat, and then I walk in. It isn’t the end of the world. You can make adjustments, and as long as you can keep them safe, take the minor inconveniences in stride, let them settle, then fix you’re troubles. It will be ok.
Long term I'm sure things will work out. Funny story...I wasn't planning for RIRs or leghorns...we asked for 3 barred rocks...I definitely prefer 4 chickens over 3 chickens, I got an extra free chicken...I'm not picky about breeds with my first ones so I'm ok with it...my short term issues are:
1. How the hell am I supposed to get stuff set up properly in the coop/run.
2. How will I collect eggs without the chickens escaping.
3. Securing the area around the coop with a fence (made out of chicken wire, probably) so that if they do escape they can't get too far.
I am not going to let them do ANY free ranging, supervised or otherwise for a WHILE.
I've calmed down for now. Tomorrow I will sit with them near the run and toss in treats from time to time. If this was up to me I would have built my own coop and gotten chicks, but yeah.
 
I will be calling a friend tomorrow to ask questions, and I have other friends right down the road if I need hands on help. my main question right now is: how high do they actually fly? would a 4-5 foot fence contain them? I knew they could fly, but I've never dealt with birds who are truly terrified, just ones that are annoyed about being picked up. What I really need is to move them into a dog crate so I can move EVERYTHING around all at once, but I don't have a dog crate and don't know how I would get them into it.
 
Can you go out there right now, maybe with a flashlight, and move the feeder and waterer into the run?

That would solve one of your problems right now.

If you do not bump the chickens, there is a very good chance that they will stay where they are, because it is dark.

For the next few days, vecause the chickens are afraid of you, they will probably try to run away from you when you open a door. So they will likely run into the coop while you tend the run, and into the run while you tend the coop.

For collecting the eggs in the coop, if the chickens do not all go into the run: put a treat in the run so the hens are busy, count that they are all there, then get the eggs while they eat. For this purpose, I suggest a small dish of wet chicken food for the treat: hens often like it, and they have to stay right there to eat it. Or grass/lettuce/greens that are cut up really small. (If you give big pieces of anything, one hen will pick it up and run off with the others chasing--fun to watch, but not good when you want them in a specific place.)

For teaching them that people are nice: if you walk up to the run and drop in a treat, multiple times a day, it will help. Again, I like small amounts of green plants, because they can eat a lot of it without it hurting their health. And because what they don't eat will dry out into hay, which is less appetizing to them--so they're always eager for more fresh greens.
 
I will be calling a friend tomorrow to ask questions, and I have other friends right down the road if I need hands on help. my main question right now is: how high do they actually fly? would a 4-5 foot fence contain them? I knew they could fly, but I've never dealt with birds who are truly terrified, just ones that are annoyed about being picked up. What I really need is to move them into a dog crate so I can move EVERYTHING around all at once, but I don't have a dog crate and don't know how I would get them into it.
Leghorns can be exceptionally good flyers for chickens. I read a post years ago from someone who thought her chickens had all escaped or been stolen, only to look up when she thought she heard something and discovered they were all roosting in the VERY tall tree next to their run :) They are very good layers, and very good foragers, and always alert to any potential threat - they are considered flighty because they basically think everything that moves is a threat. They stay alive that way.

So, the way to accomplish things is to always close the gate into the run immediately after you get through it before you try to do anything else. If there is ANY chance it can latch in a way that traps you inside, fix that first. When you go through that gate they will almost certainly go to the other end, under or into the coop, especially at first.

If you can make your fencing around the run 6 feet tall with a cover, so you can walk in without crouching, and keep them inside, you will be happier, and it looks like that's actually what you've got, if I'm understanding your description correctly.
 
Leghorns can be exceptionally good flyers for chickens. I read a post years ago from someone who thought her chickens had all escaped or been stolen, only to look up when she thought she heard something and discovered they were all roosting in the VERY tall tree next to their run :) They are very good layers, and very good foragers, and always alert to any potential threat - they are considered flighty because they basically think everything that moves is a threat. They stay alive that way.

So, the way to accomplish things is to always close the gate into the run immediately after you get through it before you try to do anything else. If there is ANY chance it can latch in a way that traps you inside, fix that first. When you go through that gate they will almost certainly go to the other end, under or into the coop, especially at first.

If you can make your fencing around the run 6 feet tall with a cover, so you can walk in without crouching, and keep them inside, you will be happier, and it looks like that's actually what you've got, if I'm understanding your description correctly.
I could probably do some tall fencing with a tarp to cover...this would have to be temporary. I specifically didn't want leghorns because they are very skittish, but here we are. Any fencing wouldn't be for free ranging at this point-just a 'safety net' for if they get out. Do you think that my best bet would be to move them to a dog crate or something of the sort so I can move things around? We got a puppy playpen to use that is about 4 feet high, but it will not work apparently. I don't want to train them to be afraid of me in any way, but I also don't want them to escape.
 

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