A/C not working properly and transmition jerking in between or in and out of gear

Need help bad. 07 6.o Diesel e350 superduty. Had
metal shavings in Orpheus tube. New compressor
was shot. Changed out all components -
compressor, dryer, condenser, evap, and flushed
out lines. Vacuumed out system and recharged to
oem specs.  Now my compressor kicks on after a
while and transmition jerks while trying ro shift in
next gear. Can be driving for a while in the city and
will get a lag in engine rpm them compressor will
kick on and start working bloowing cold but
transition will still jerk occasionally.  while on the
high way at high speeds compressor will kick off
trani will jerk back and forth into speed a few times
then no cool air out of vents. Going crazy need
help. Logged in to Just Answer checked all the
voltages to and from dryer to the compressor.
Determined PCM was shot. Changed it but still
having same problem. Can someone please shed
some light on this issue. It's my work van and is
getting frustrated. Don't want to end up damaging
trani.