I think I understand what you are trying to do. There is no way you can have enough room in a 2x4 area for roosts for 6 chickens, nests, plus food and water. Since you want a tractor I understand the need for it to be lightweight but there are physical limits. You just can’t cram all that stuff in there. That area would probably give you enough room for a roost and nothing else. Even that will be tight if you lock them in there overnight and don’t open it up in the morning pretty soon after they wake up, but you can probably manage that. You may consider your tractor predator proof and not lock them in there at night.
I’m guessing that the overall size of your tractor is 4’ x 8’. That’s pretty tight for six chickens. From when I had a tractor I think you will wind up moving that really often due to poop build-up. It will probably start to stink pretty quickly, especially if you have wet weather.
I’m also guessing it is four feet high. That doesn’t give you a lot of room to work with but it does some. Your roosts need to be higher than your nests, otherwise you have a good chance of them sleeping in your nests and giving you poopy eggs. I’m also guessing you are planning on a flat roof. That’s really not a great idea. If water sets up there it will rot the roof or, if you don’t have a complete solid roof, it will leak. You need enough slope on it for the water to run off.
Some suggestions. Put a roof on it with a slope that directs the rainwater away from your tractor, not into it. Put ventilation openings at the peak of that roof. I really like an overhang so you can leave the area under the overhang open without rainwater getting in though cover it with hardware cloth to keep predators out.
Put your roost in the area you have already boxed in. Leave the bottom open so the poop falls straight to the ground. No need for you to clean anything, when you move the tractor you’ve taken care of the problem of poop build-up. That will give you great ventilation too. They should have no problem getting up there but if you wish you can put an intermediate step, another roost type pole or board, offset a foot horizontally and half way up to the roost.
On the other end of the tractor, put your nests. For six hens two will be plenty. Make them lower than the roosts but keep them a foot or more off the ground. That gives them access to the area under the nests so it does not take living space away from them. You don’t need to box in all of this end but some extra shade might come in handy. Two 12’ x 12’ nests will be sufficient. You should be able to feed under the nets and keep the feed dry. The water can go anywhere they don’t poop in it from the roosts.
These things can get heavy fast. You don’t need to use 2x4’s when framing out the nests. 2x2’s or maybe 1x3’s can work. You don’t have to use plywood either, though 1/8” plywood is not real heavy, just make sure your wire gives you strong sides to keep predators from breaking the plywood. You can also look for some type of plastic to box this end. Weight can be a huge problem.
And last, I suggest you consider a plan B. I tried a tractor once and gave up on it. Tractors are a commitment. You have to move them when they need to be moved. I had eight chickens with a tractor that was in two 4’ x 8’ sections I could move separately. I had to move that every 2 to 3 days, otherwise it would quickly start to stink. Wet weather was the worst. My chicken density was less than yours will be. Will you always be around or will you need to find someone that will move it for you if you take a vacation? I don’t know where you are but how suitable will his be in the winter?
One possibility is electric netting to give them a much bigger area during the day. They are still vulnerable to flying predators but electric netting when set up right and properly maintained will stop practically any ground based predator. Some people have problems with flying predators but a lot don’t. I use electric netting and it is really effective. With this set-up you’ll still probably be moving it a lot but you’re talking weeks, not days. You can lock them in your tractor at night for predator protection at night if you wish. I’ve had my electric netting a few years and my only loss wat to an owl when I was late locking them up one night.
Another possibility is to build another larger permanent coop where you can leave them locked up if you travel or if your winters are not suitable for a tractor. It could even be a larger secure run with a gate big enough to move your tractor inside and use it for your coop.
I really do suggest you consider a plan B, have something in your back pocket just in case you need it. A lot of people don’t appreciate the time commitment they make with a tractor this small. When it needs to be moved, it needs to be moved.