ford 2002 2.0 sohc spi . runs smooth on three or four starts then will run rough

2002 ford escort se 2.0l  SPI .
car came in with the number four valve seat fractured . the top of the number four piston was beat up. cylinder held compression .
change head ,timing belt ,  and  water pump. clean three injectors and replaced number four injector. New plugs and wires and fuel filter 

started the car after head replacement and it started right up and ran smooth. road tested vehicle with no problems . turn the car off . it sat for a half hour or so. Started the car and it started right up but it ran rough. Cleaned mass airflow sensor . No help. cleaned all the connectors at the ECM and it cleared up. released the car back to the customer.

After two months the car came back with a check engine light  on .Thet code was IMRC STUCK OPEN..  the car was ALSO making an engine noise.  The engine noise was a worn keyway on the harmonic balancer . Replaced the balancer and the engine noise  and the code were gone. 
test drove the car .No problems. came back to the shop and let the run for an hour . . check engine light came back on this time DTC P1745 transmission line pressure too high..
Clear code and it came back . I changed the camshaft position sensor because I thought the PCM could not find number one cylinder.  I can not get the car to run rough again. 
other than performing a pressure check when it does run rough and using my scanner to verify line pressure, Does anyone else have any troubleshooting advise to try. 

When it is running rough:

Is it in OPEN or CLOSED loop?
Are the Upstream O2 sensors switching rich/lean?
What are your Long and Short Term Fuel Trims?
 

it is in closed loop and yes the o2"s are switching .

I will try and attach the scan data

Send me your email address . these are SCM files shop stream files