I personally wouldn't worry about the trans right away.. Me and my brother both had lmls with 10mm cp3 conversions and he had a 475 over stock and I had a single 468.. My stock transmission took that fine for a good long while and his did too.. If you don't go out and beat on it every day it should be fine BUT, you should always be ready to get it built at any time lol..
I'm sure the tuning was set extremely mild with twin on a stock trans.
to the OP, trans first, then twins