Drive to store and car wouldn't start jumped start and smoke from startervand nothing not even crank

The vats system was by passed. And charging system was up down. To start the starter was sticking the battery wouldn't start car got a jump and smoke came from starter but the car never turned over like no power at all someone said solenoid but I was thinking the resisters were messes up ( from bypass vats)

Cold Engine surges at 1000- 2000 rpm and has rough idle till about 20 min., then it idles and runs normal. I unplugged the MAF sensor and the engine smoothed out and ran normal. Replaced MAF sensor with remanufactured MAF sensor ( not A/C Delco ) and the engine runs perfect. However, if I stop the car a few minutes and restart the warm engine, it surges badly, then stalls.Pretty much undriveable.

Im pretty sure I have a bad cv joint the car clicks when I first take off stop or turn corners

changed fuel pump and filter same problem

I have tried removing the Glove Box but all I find is a large bracket that when the bolts are removed will not come out.

Change Trans oil and filter

both drivers side windows won't go down doors won't lock