we just harvested the last of our latest batch yesterday. while there are things that you can do to help with what you are talking about, this is pretty "normal" behavior. I have found that raising the water, as you have and raising the food helps and keep them as far apart as possible, I like a good 7' at least, between them and I think longer runs are better for CX than square, even adding a turn, like an "L" shape with the water and food around the corner from each other at opposite ends is good. as soon as enough make it around the corner and can't be seen, the rest come like a pack of wild elephants in full charge mode. I use a mother heating pad and allow them 24/7 access to food without issue... much better than a heat lamp in the early weeks.
using a nipple waterer has helped me keep the water clean, which helps them from getting diarrhea. also, some feeds are super high in protein, sometimes if they get the squarts, I will add a lower protein formula like an egg layer in and that can help.
also, depending on what strain of CX you got, you should know that some are much cleaner and healthier and require less coddling than others. I like the COBB 500, you have to ask about the strain... then again, for 25 cents, I'd say you've got great birds!
their underside hardly grows feathers, it's just part of their breed and part of the fact that toward week 4-8, they spend more and more time lying down because of the weight they carry. I've found that there are ways to keep them more active and cleaner but that invariably, in the last week or so before harvest they are plowing through so much food and producing so much waste it's hard to keep up with it all. I use a deep litter method with partially pre composted wood chips, I "peel" away the mat of droppings that form and with it comes enough carbon/wood for the composter and in it goes, but it will stink to high heaven if you add too much fresh manure at once to a tumbler composter.
as for harvest, you'll notice a precipitous drop off in how much they eat, somewhere around week 8. you can get a bit more weight on them waiting till week 9 to harvest but not a lot, I harvest between 8-9 weeks.
they look great, good luck. and if you want more details, check out the link below.