From the dimensions that you've given and according to frequently quoted space requirements you have overall enough space for nine large fowl chickens. The limiting factor is the run space (90sqft) which limits you to nine LF chickens @ 10sqft per bird. The coop dimensions (48sqft) can handle twelve LF chickens @ 4sqft per bird. Going up to the max number of nine that the run can handle will leave some nice room in the coop for them (more space = happier chickens). Your setup looks good...it's fantastic for just two chickens! Something tells me "chicken math" might kick-in, though, so just try to stay below nine of them.
As aart said, any thing that takes up floor space inside the coop reduces the number of chickens that the coop can handle. Horizontal nipple waterers configured on pvc pipe take up little room and can be mounted close against a wall and can be designed to be filled from outside. If you use a droppings board you could position bucket feeders beneath the roost bars. Without a droppings board the area beneath the roosts may or may not be usable by the chickens. Or, you could do as you mentioned and look at the pvc pipe feeders.
Your covered run... Will you be locking up your chickens at night within the confines of the coop (closing the pop door)? If so, you might can bet by by using chicken wire or avian netting to block off hawks, falcons, etc.,. How tall are your side fences to your run? If the pop door will stay open into the run all of the time then you will need to use something heavier than that.
As for your run fence....in my opinion, it needs beefing up. Dogs and large raccoons will tear/chew through hardware cloth. If you were to get a 5-6 foot wide piece of 2x4 welded wire (or better yet, woven wire) fencing and cover the lower 3-4 feet of the sides while bending out an apron of 18"-24" horizontal to the ground you would thwart dogs chewing through and digging beneath the fence. The hardware cloth will turn most predators away but if you get a frenzied dog or a big old board coon that's excited over a chicken dinner, well, they'll go through the hc.
Going back to *if* you will be leaving the pop door open 24/7....I would only sleep good if I had 2x4 fencing covering the run with a sufficient apron extending out from the bottom of the fence and a hard threshold beneath any gate/door leading into the run (simply a heavy timber buried beneath the door with some apron wire extending outwards or either a trench dug and concrete poured into it). The area beneath gates can develop a large gap from simply walking on the ground there...it can get big enough that critters can easily crawl beneath it.
Best wishes,
Ed
