I'm working on this conversion but I have a question about linking two batteries in parallel. I have a bunch of 11.1v 2000 mah batteries from my helicopter days. I'd like to make good use of them. Is linking them in parallel a good idea or will have problems with draining them at uneven rates? Does anyone have any suggestions?

Paralleling them is fine if they are the same age, capacity, C rating etc., or if you don't exceed the C rating of the lesser of the two.  I use mine in 6S2P and 9S2P configurations all the time.