I'm in the process of the same thing. I chose to start with a 16,000 mile 2004 transmission and changed the tailshaft and planetary ring gear since I was in there anyway and didn't want or need a retune.
I also chose to go wild with the build though adding additional frictions and steals, replacing all of the lip seals inside the drums, replaced the scarf cut factory direct drum sealing rings with solid ones, switched to an aftermarket 4 seal 2-3 accumulator, upgraded to the sonnax OD servo pin, upgraded to a high carbon OD band, upgraded to the sonnax pressure regulator valve, replaced the mlps, better torque converter, large transmission cooler, lpw deep transmission pan, all new seals, jmod, etc...
I don't want to have to replace it again for a long time and I wanted to do it right the first time.
Ultimately you'll have to make the choice on how far in your comfortable going and how much you want to replace/upgrade/leave stock for your application.