Speedometer keeps around 50mph after warmup...????

You have replaced the entire drive train and it still does that? If you are saying the vehicle is going 50mph without even touching the gas pedal, that sounds like a high idle situation, like about 1500 rpms. Normal idle when warmed up should be only 650 rpms. I would scan for fault codes before replacing any more parts. I believe your truck is OBDII compatible, being 1996 and newer. In the mean time look for a massive vacuum (air) leak on the intake side of the engine and try to get the idle speed down.

Well it's a manual trans, but yeah! Now it will cool-down, and run normal (like it always should) while still cooled-down.... and the idle has an auto-adjust design that goes to a higher RPM when the vehicle starts moving at about 2-5mph, even in neutral... I already replaced the air-intake, so no leaks to concern about there... So maybe there is an error in the replacement trans, it was a used one, I just can't believe it would seem to be exactly the same.... seems really unlikely to happen!