If you look at the fuse panel there are two silver 30 amp fuses on the right side or there should be. they are in the blocks marked POWER with the arrows pointing to the right. One is for the windows the other is for the power door locks. Not sure which is which try both hope this helps.
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first thing check all fuses, if ok your problem more likely rear tail lens circuit board where your bulbs push into. the sockets over heat and melt . this is a problem with these trucks from 1988 to 1999
Those values and most everything else you need for DIY work are contained in the Haynes manual for your vehicle.
We have one with each of our vehicles and not only give you the info needed to do repairs yourself but also get an idea of how much work a specific repair should (or shouldn't) cost.
'88 Chevy pickup manual
You can also buy these from auto parts stores for a few dollars less and sometimes on eBay for even less.
Did the transmission you put in have the the pick up on the output shaft. Pull out the vss and see if the pick-up is on the shaft or a speedo gear is on the shaft. If it has a gear, you will have to change it to a pick up wheel. The older 700 transmissions used gears.
if fuses chk.out ok i would have to say its the drivers side controls went bad. windows, door locks, everything runs thru drivers controls. even though you said buttons chk. out ok i can't think of anything else other than a fuse, unless the wires came loose from the maine controls or maybe there coroded. hope i've ben some help. OLD SCHOOL.