Reoccuring obd ll codes after rebuild

I just rebuilt the power train and overhauled
the engine of my 2002 ford mustang base
model convertible 3.8L V6 due to it failing its
last emissions test as well as having abrupt
periodic power loss/accelerator lag even
with the accelerator buried to the floor. (This
would happen on flat stretches or hills it
didnt seem to matter) So i replaced the egr
valve and the egr pressure sensor as well as
the egr solenoid plus the ignition coil pack
and spark cables and spark plugs as well as
doing an oil change and replacing the air
filter plus the fuel pump and fuel filter plus
the injectors and the accelerator cable plus
the exhaust headers and exhaust system
with catalytic converters and muffler. Then
because i was already so far into her i went
and replaced her brakes and rotors and
shocks plus abs sensors as well as tires and
wiper blades plus the fuses and battery etc
etc then got her an alignment and did a
compression test.(no loss). as well as
another obd scan from my bosch 3100 obd
ll reader.(no codes or dtc's) Well she passed
emissions and was acting like she was
brand new for a few days but then out of the
blue she starts up with the same problems
that led to the rebuild..... Thoughts anyone?