I've seen guys use a electronic fuel pump to flush fluid through the trans. I would drop pan, change the filter, put a new converter in it, install your shift kit, and throw it in the truck.

Check your shift kit, I know some of the ones for older th350's/700r4's recommend type-F after the kit is installed. If not, throw regular dex3 in it and call it a day. OR run something like royal purple (their oil is garbage, I really like their trans fluid)