Engine trouble with daughter's 97 SC2

PLEASE....someone help me, I'm at my wit's end. My story in brief. Daughter is in college, she bought a 97 SC2, engine threw a rod, garage installed a 50,000+ engine in it.....then the engine problems began after about a year. The engine will "surge" or "miss" or "skip". This becomes pretty bad at times and gives "misfire" codes, etc. We've had the codes read an had a garage AND a Saturn dealership replace the following:
Plugs/wires/coils/valve cover gasket/coolant temp sensor/engine temp sensor/O2 sensor in manifold/fuel pump/cleaned injectors and valves. Some of these things have been replaced twice already, but it will still skip after awhile and give O2 codes and multiple misfires.

What gives???????? Why can't the Saturn place fix my car? What can they possibly be missing? My daughter goes back to school soon and we've sunk over a grand in it to no avail. After their last round of replacements, the car unloaded a ton of carbon buildup and ran better for awhile, but then it started misbehaving ALL OVER AGAIN!! I'm begging you, help me out.....

Replace the O2 sensors.

the pintle in the EGR valve is probably at fault. This is probably sticking causing tps to go slightly out of range fouling the O2 sensors.
Good luck........p.s try a diff saturn dealer.

Also could be a clogged Catalitic converter, like a domino effect.