I've been wrestling with a bad tranny for 2 years and ended up replacing it with a used low mileage unit.
If your revs dont shoot up, while the car hesitates, you probably have engine running issues. If your tranny drops out of gear into neutral mid corner, or when the tranny is not warmed up, you may be low on fluid. If the revs shoot up, and the tranny catches, your tranny is slipping, and it will die sometime soon.
I had a bad ccv, so my valve cover gasket was leaking. I replaced the vcg and ccv, but still had high fuel trims and erratic shifting behavior. I already replaced all the vacum tubes, rubber stoppers, oil filter housing gasket, new disa etc. Still high fuel trims and rough idle. I ended up replacing 6 o rings on the intake distribution piece, and flipped the oil filler cap gasket(it was flattened and will eventually replace it). Voila, fuel trims back to normal and shifting back to normal. You should go through the engine and replace all rubber parts anyway.
You should check the tranny fluid level and top off if necessary.
Reset engine and tranny adaptations, and you should be good to go.
Keep your eye on torque converter slip, because it will overheat the tranny and in turn, leak fluid from torque converter seal as the seal goes bad. My tranny cooked itself from losing fluid.
good luck:thumbup:
Edit: First things first, check to see if you have any codes in the tranny module. If you have gear monitoring codes, it's probably toast. And I forgot to add, my alternator was bad, and it was causing weird electrical issues with voltage spikes. FCP euro has a bosch unit for pretty cheap.