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99 Dodge ram 2500 with a Cummins automatic transmission not shifting

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1my alternator went out a couple weeks ago and when I replaced it my transmission now is not shifting it's like it's setting in either second or third gear and won't do anything or checked all the fuses all the relays I ended up having to put a external voltage regulator on because my voltage regulator wasn't charging my system and now I can't go over 55 60 because it will no longer shift what could be causing that what can I fix that with
 
Couple things come to mind. Some of the 24v folks might have a better starting spot.....

Replacement alternator could just be junk. Alot of the replacement are for these engines. Rebuilding what you had would have been the preferred option.

The new alternator could have some really bad AC noise worse then the last one.

There are known OEM harness issues with grounding which include the alternator circuits, sounds like you need to complete the wiring mods to repair your grounds. When you get it to it you will find it amazing they make it as far as they do.

As a coincidence the transmission relay could be bad you can swap that with the spare one. Dont think so, but never know it's an easy swap.

Do a as found AC voltage check with the current Alternator. See what you come up with.

A bunch of us split our time here at the TDR and on mopar1973man.com, over there it's a few bucks to sign up for a membership the 24v has a lot of wiring diagrams and articles on exactly what you need to do for the AC issue.

If you get it all the wiring sorted you might wind up ditching the external regulator that could just add issues to the trans issues your seeing.

If you happen to still have your original alternator save it and get it rebuilt you can do it or you can have a local.place do it. Rebuild items are cheap.
 
If you have disconnected the battery then the computer has lost the throttle position sensor calibration. It will not let the transmission shift without recalibration: Reconnect the battery, place the ignition in ON (don't start the truck), slowly press the throttle pedal through it's full range of motion twice, turn the ignition off. Restart the truck and the transmission should now shift normally.
 
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