I am a Gold Certified tech, so I'll see if I can help you further.
I'm sure by your description, they have done all the normal things, so I'll throw some more ideas at you.
Can they isolate the miss to one cylinder by disconnecting each injector in turn?
At that point, it will miss on one cylinder only, if it misses intermittently on 2 cylinders, then the one they disconnected is not the cause. They need to find where with one disconnected, it only misses on that cylinder.
When they did the ECM replacement, did they do ALL the programming and setup procedures?
Compression may be ok, did they perform a cylinder leakage test?
Have they inspected the camshaft and roller rocker arms for wear/damage?
Have they taken a fuel sample and checked for any water?
Have they checked the low pressure pump supply pressure?