Diesel Bombers - Voltage problem

I've got a 94 12valve i purchased recently that as far as i know is all stock besides the fuel pump bein turned up. Its having voltage problems. If i charge the batteries the volt gauge sits at about 12volts and check engine lights on i can run it for maybe an hour before it starts to drop. I've bench tested the alternator its workin fine they said. i've cleaned all the grounds, battery and alternator connections. It went away for a little when i cleaned the battery connections (voltage was were it should be just over 14 and check engine light was off) but after drvin it and turnin it on and off the check eng. light and volt was low again. Also when i changed the thermostat everything worked right for about 20 min of running and then the check engine light came on, voltage dropped, and the temperture dropped too (while drivin down the road). I tried the turnin the key on and off three times method to count the check engine light flashes and get a code and came up with the numbers 122441373755. i tried lookin up the codes and the only one that i found may be the culpritt is the 441 code which said unswittched battery supply circuit. Coundn't find any info on how to fix that, any info or input on the problem would be great cuz i'm gettin stumped (tryin to avoid the spendy trip to the shop). btw i'm still learnin the wrenchin. oh and also the tranny shifts weird, thought it was the tps cuz it wouldnt lock the converter on its own and shift into OD. i've been runnin it with OD off ans convert lock switch to shift to 3rd and then turnin the OD on at 50mph for it to shift to OD (bought it that way). I put a new tps in and it shifts now but it will pop out of convert lock and OD off and on if i drive it normally without switchin it all manually.