possible ford transmission problem

ok guys here is the story, i have a 98 ford expy with the 4r70w transmission. recently i lost 3rd n 4th gear completly so i decided to change transmissions i bought a garenteed good one from a local j.yard. in between taking out the old n putting in the new i had to move the expy, i turned the key over to use the stearing wheel, when i did the o/d light began flashing. so i get it moved and remove and install the transmissions reinstall everything and connect everything n so forth. now when i start the expy it idles perfectly, about 1,000rpms but when i push the gas it hesitates but will eventually idle up to about 4,000 rpms. when i put it in gear it bogs way down to like 4 or 500 rpms and barely moves as a result of the low rpms. i had a local friend/mechanic take a look an he said everything looked ok as far as the work i had done to it and the only problem he could find was that there wasnt any power coming from the pcm to the transmission, yet all the fuses n wires are ok.?? also if i put it in 4x4 low it will move fairly easy as if there isnt any problems. btw the O/D light is still flashing and throws the codes for literally everything in the transmission. any ideaas to check or so forth would be greatly appeciated. i have a theory that because i turned the key over to move it threw the codes because i had everything d/c from the old transmission, and now it wont send any power to the transmission till i have the computer flashed and that the transmission is stuck in a higher gear like 3 or 4th or the torque converter lockup is engaged because of the "no power to the transmission" ordeal? it also has new tps maf iac fuel filter n pump air filter

You need to clear the history and then let the pcm do it's thing with everything connected. That should help pin point your troubles. Good luck!

i tried by removing the battery terminal for various lengths of time but when i start it the o/d light automatically starts blinking. do you think if i had a dealership flash, "reprogram" ,the computer that it would run ok?