We just recently swapped the engine in my 1994 f350 (460 7.5l) and it was running great for a while but it randomly didn't want to start. The fuel pump would run and run but wouldn't turn off. If I could get it to start it ran like a champ, no problems at all. I figured it was a bad fuel pump or a bad filter so I took it to the shop with the parts and had them swap both fuel pumps and the fuel filter. when I went to pick it up it took them over an hour to jump start my truck. when they got it started it ran horribly, spitting and sputtering, black smoke coming out the tailpipe like a diesel, and it wouldn't move when he put it in drive unless he floored it and even then it wouldn't even get up to 15mph. After doing a lot of testing and digging we decided to replace the ECM and it fixed most of the problems, the engine ran good (after new spark plugs) and problems I didn't even realize where there are now fixed but the transmission still isn't acting right. 

After doing some testing it seems that when the transmission is put into drive it starts in 3rd gear. If I put it down into first it has more power than when I put it in to drive but still not as much as it should have. 2nd seems to have more power from a stop than first does. I've been able to get it up to 60mph by shifting down to first, then to second then in to drive. it seems like the overdrive is also not working and after I put it in to drive it just sits where it is at, won't downshift or upshift. I'm really confused about what could have possibly happened. It seems odd that it went from not starting to transmission doesn't want to shift on its own. I've checked the transmission fluid and it was fine, possibly a little high. 

so far we have replaced the neutral safety switch.

I don't know enough about how the transmission is controlled to know what part or parts have broken to cause this. I have some random electrical problems throughout the truck so I don't know if it's a bad ground? I've also been recommended to look at the solenoid pack. 

I'm new to doing stuff like this, swapping the engine wasn't too bad but when it comes to transmissions I'm completely lost. I'm looking forward to your advice. 

truck: 1994 F350 4x4

engine: 7.5l 460 big block

Trans: E40D (I think)

-no relevant check engine codes.