I cannot see how one bolt missing from the transmission would make a difference in shifting.Did you check the fluid? After the car has been driven your fluid level should be at the FULL mark.Not above it, or below it. Also,if your replacement trans came from a bone yard, That could be the problem".Most junk yards offer a warranty for a few dollars."
SOURCE: ford 2001 explorer sport transmission slipping 2nd to 3rd gear
I agree with the shift solenoid being the problem.
SOURCE: 99 dodge ram 1500 4x4 5.9l tranny problems
Take a look at the down shift cable and make sure its not broken especially were it connects to the throttle linkage.And maybe try cleaning the electrical plug that plugs into the trans.Its about a 7 to 9 wire plug.They tend to collect water and short the wiring out.
I’m happy to assist further over the phone at https://www.6ya.com/expert/joe_a3369546f8067589
SOURCE: 99 dodge ram that jerks between 40 and 50 mph
Bring it back to the transmission shop and have them test drive it with the scanner to see if the Throttle Position Sensor (TPS) needs to be replaced. A worn TPS will case the transmission to have shifting problems, the TPE sends voltage signals to the PCM and will control the transmission shift points and firmness. If the TPS has a flat spot and the voltage is down at the point where the transmission needs to shift, there may be a conflict of shift program and needs to be addressed. Good luck and keep me posted.
SOURCE: How to change transmission fluid and filter. 2004 dodge ram 3500
remove trans oil pan. there you will also see your trans filter,
SOURCE: 1996 dodge ram 2500 auto transmission not shifting properly
Well, first do the service. Pull the pan down and look for metal shavings. If there is metal shavings your in for a transmission. If not, you may have a problem with one of the transmissions shift solenoids located near the valve body.
P.S. The Duramax has the Allison 1000 transmission not the dodge cummins and they are one of the best trannys on the market.
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A clicking sound, could also be an "Inner, or Outer C V joint
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