I believe it on the learning curve, it's so different than the Banks chip. I never really though about that part of custom tunes.

What are some tips on running it most effectively/effeciently?

Just try to keep the EGT's and Boost as low as possible for max efficiency.

I know sometimes it just is not possible or safe but keeping speeds down help dramatically.

Doing the TransCommand un-install isn't that hard. Just download the install instructions and go in reverse. I did mine in about 15 minutes.