My 99Dakota3.9V6 4x4 SLT excab w/84,000miles, ran well plenty of power only thing was since i've owned it has idled low as if to die when shifting into reverse. But just had it parked for two weeks to change water pump, alternator an battery. I took it back out an now starts an idles ruff, doesn't want to get out of its own way, doesn't want to shift barely can make it to speed an at high rpm's and smell fumes. Thank you
-also I was haveing a problem with low oil pressure an at low idle drop to zero.I am replacing oil pump which I believe will solve problem
Don't rip into the oil pump until you are sure it is bad. It's a big job. Check pressure with a mechanical gauge. Most parts stores will lend or rent them. It screws into where the oil sending unit goes. I would hate to see you rip half the engine apart to find you needed a 20 dollar sending unit. Keep in mind, if there is no knocking or ticking from the engine, you have oil pressure.
As far as the other problem, if you had the battery disconnected for a period of time, it will take the computer some miles to relearn everything. And the idle issue, check for vacuum leaks and check the idle air control valve (IAC). It is responsible for the idle speed.
One last thing. To remove the waterpump is a pain. I know you had to remove the AC compressor and alt as well as their mounting bracket. I hope you replaced the bypass hose under there. Also, the temp sending unit is mounted next to the heater hose right there. Check to make sure you didn't break it. It is small, and can break easily. That could have an affect on driveability.