I put a 5.9 and 46re in my jeep tj. Had some issues with a couple pcm and now I have it running good with a MP Dakota r/t 2wd pcm. I didn't think the 2WD would matter at the time but the 46re shift points are controlled by the pcm, so what will happen when I put it in 4low?

The "shift points" are not necessarily controlled by the PCM. The governor pressure is really the only pressure controlled by the PCM. The throttle valve pressure is still determined manually. I'm not sure a PCM from a 2WD would really make any difference on the way it shifts if everything else is plugged in, hooked up and working correctly. The controller doesn't care if its in 4WD or 2WD to control governor pressure.