Unless you put it in EXACTLY the way it was before..... timing is likely off. On that one, I think timing is actually controlled by distributor position. Might wanna put a timing light on it, and see where you are at. Not sure what the procedure is for setting base timing on those......

 

Presuming it's the same for the 3.9 (and the 5.2 and 5.9 in Rams for 1988);

1) With the motor off, connect the timing light to 12V, chassis ground, and Cylinder 1.

2) Start the motor, let it warm to normal operating temperature.

3) When it's warm, disconnect the Engine Coolant Temperature sensor (the two-wire one, usually on LA motors to the driver's side of the thermostat housing.)

4) Set ignition timing to the proper mark according to the EAR label; typically for this vintage, it's a default of -10*. (That's 10 degrees before top dead center, or BTDC). Side note: If you don't mind running a higher octane fuel, you can run it up to -14* or so; do so at your own risk, though.

5) Reconnect the ECT sensor.

6) Turn the motor off.

7) Disconnect the timing light.

That should do it for a LA motor.

 

I timed it by ear. I did check with light. Was just a tad out. Set perfect now. No change.

 

I reread the first posts. What comes to mind for me is that you may have the alternator wires crossed. IDK the electrical flow of the motor other than generally but if the wires are right it seems like where ever the power flows from the alternator is the path to follow to look for what it is affecting. Oh yea check the fluid level in the trans and if it is one of the 42rh varieties try unplugging the solenoid on the driver side of the trans just behind the TV cable linkage to see if it runs ok with the alt connected. You won't have OD.

 

It is a molded plug to hook up alternator. Then the positive main wire extends from that. Tied removing plug on transmission, it had no change. Was a little backwards the way i got to it, made it hard to put back on.

 

The alternator wire goes to the fuse block under the hood. I will pull that off and check things there.

 

I don't have any idea but I suspect something is shorting in that fuse block or one of the relays is failing.