Q: I have a 2001 Spyder GT that has not been running properly. I replaced the cap, rotor, wires, plugs, and plenum gasket

The car seems like theres a lifter sticking but after you run it for a minute, it smooths out and idles normally. When you shift it into gear in either drive or reverse, the car will lose rpm and runs rough and shake. On the road when you accelerate, it starts off in first relatively normal but after that there is a big lack of power. You can put the pedal to the floor and nothing will happen besides it might shift down a gear or bog out and sputter. It runs about the same with or with out the mass air flow sensor plugged in and I believe an O2 sensor is bad. Ive also had the timing chain done and the water pump. Any help would be appreciated because I have more money into the car than its worth and I don't want to keep throwing money at every possible problem. Basically, the car has no power. Shakes at low rpm. And it starts noisy until it warms up

My car has 125000 miles.
My car has an automatic transmission.