2001 Lincoln Continental Engine runs Great in Park/Neutral

My mechanic cannot figure out exactly what is wrong with my Lincoln. I was driving it and all of a sudden it strted running rough. Woud strt but run rough all the time, park, neutral, driive. He found a broken valve spring replaced it and got the engine to start up and run great while parked. On the test drive it runs very rough and stalls out. Place it in park it starts up runs fantastic put it in drive and it runs rough and wants to stall out. Now 3 mechanics have looked at it and can't figure out whats wrong. No error codes on the multiple scans that they have done with different scan testers. Now the mechanic tells me two cyclinders seem to be dead but there is good compression, spark and fuel to these.
Now he says its all he can do. He doesn't know what's wrong? I have been going to this mechanic for 30 years and there has NEVER been anything he can't figure out and fix. WELL UP UNTIL NOW
Can you help me & him?