Hi Lizzylou!
I flew BA from ATL to LGW with my two cats in October 2006 - things may well have changed since that point, so I would always advise contacting BA World Cargo (whom I found to be more than helpful during my planning) to make sure, but here's my thoughts on your various questions (and there are more than a couple of posts on this forum about my experience):
1. What size crates (and dogs) do you have? I would always, ALWAYS err on the side of too large - my 11-12lbs cats looked ridiculous in the Petmate Medium dog crates but there was no issue about size once we reached the cargo centre and I'm sure the boys appreciated having the space to move around. Unless I've missed some massive redevelopment in the College Park/Old National Hwy area in the past few years, I think you'd be looking at a run to Southlake or thereabouts to find a Petsmart or Petco to buy a new crate, so I would definitely take that into account!
2. I would ask this of BA World Cargo directly, as when I flew in October 2006 the APHIS form served this purpose (and was required by BA) but those who have flown BA since that time have posted that BA no longer requires this form.
3. Are you talking about the form issued when the rabies vaccination was given? If so, mine was signed in black ink, because my cats had their shots well before we started the PETS process and we had no idea that ink colour might be an issue.

I made sure the EU 998 form was filled out with blue ink - that was the only one about which I was specific, and both the airline and DEFRA accepted all of my paperwork, no questions asked. I think the USDA vet in Conyers put a raised stamp on those pages when she was endorsing everything else, and she didn't say anything about the ink colour....
4. I had a hamster bottle on both carriers and BA was totally fine with this.
5. My guys have HomeAgain chips - again, no worries there, totally readable.
BA World Cargo staff at ATL were pretty awesome, in my experience - you may have seen my earlier posts from the time about this, but we had car trouble on the way to the airport and were running severely behind - not only were they calm and reassuring when I called in a panic from Conyers to let them know, once I finally arrived they got everything done quickly and answered all my questions with a smile and just generally made me feel so much better about the whole process at a time when I was just stressed beyond belief by everything that had happened already and that I was trying to do!
Feel free to PM me with any questions - obviously things can and have changed since I flew over but I'll be happy to help in any way possible.

Good luck!