The PCM is your computer. It controls most of the electronics and sensors. The new PCM will help with the new air/fuel mixure so you can use that extra power with out hurting your engine. Also the stage upgrades do not void your warrenty. I don't know if the new parts are under warrenty, but it doesn't effect the warrenty on the rest of the car.
Were did you take your car into to get it worked on? There is a fix and they can fix it at the dealership. The problem is if you fix it at the dealership, the problem can come back. There is a fix that will stop the oil leak for good. Dealerships are not doing this fix yet. Check out the other Neon and SRT-4 forums that I posted before. They do have the fix for you. If you need the websites for them again, let me know and I will get them to you.