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I have a 2001 dodge 3500 5.9 diesel and the alternator went out we replaced the alternator and now my transmission will shift up and down sometimes, most of the time it drive normal please help

thank you for all your help, we are up and running... we had to run the cam and gear, the timing case and cover from the dodge everything else is working as it should

i have the wonderful 53 block with 17 inch crack.. so i bought a 2002 bluebird bus for the engine its a 56 block.. my problem is we swapped the 2001 dodge cummins out and installed the 2002 industrial cummins from the bus, we installed all of the dodge injectors, the computer injection pump, vac pump, power steering pump, now the dodge didnt have a crank position sensor but the bus did, both have cam position sensors.. now we have it running runs pretty good, but tach only works for 2 or 3 seconds then zeros out, i get a code for cam position sensor have changed it with 1 from the dodge truck and does the same thing check wiring looks ok worked great with 53 block just a bad water leak please help , thank you and God Bless