Over drive light flashes after about 5 miles of driving

Hello, Did you also replace the torque converter with the rebuilt transmissions? If it is not locking up, you won't get O/D. Also, are you seeing trouble codes? It seems like you have some know-how, but at some point it will be cheaper to have this diagnosed professionally.

This should be fairly easy to diagnose with the appropriate scan tool - recommend having transmission installer perform complete scan testing - this includes monitoring all Parameter ID's (PID's) via live transmission data screen. Scan tool connected while vehicle is being test driven is an invaluable diagnostic tool. TPS can also be tested with same scan tool - if problem exist within TPS - should also exhibit symptoms of extended cranking @ start-up. *Nothing* can take the place of a professional scanner - used by qualified personnel..!