Crank sensor issue or ECM or what?

04 sedan automatic transmission.
If I use either of the 2 non-programmed crank sensors the car starts and idles beautifully as soon as I turn the key, but several codes come up (P0342, P0135, P0341, and another about a speed sensor sometimes) and send it into "limp mode" and it won't shift into the overdrive gears. I don't like driving to work at 4000 rpm at 70 MPH. When I use the new programmed crank sensor it drives and shifts perfectly, but the idle is often high and usually the only way I can get it to start is after cranking for 30+ seconds after cycling the fuel pump 2-3 times before cranking. With the new crank sensor in I'm only getting P0135 code. I'm wondering if maybe the ECM isn't taking the complete learn program from one sensor to the other or something. I just don't want a shop to make me pay to chase all the codes that come with the non-programmed sensor since it is capable of starting well with the only change I make is this sensor. Any insight is appreciated, Thanks