05 Dodge Cummins 3500 random cutting out

We have a 05 Dodge Cummins 5.9L 4x4.  We
recently went on vacation and got some bad
diesel.  The truck ran rough for a couple of days,
cutting out real bad.  After several tanks and some
additive, seemed to resolve.  We got back home
and a week later, after having to get on it hard to
pull out on to a Hwy with heavy traffic, it started
cutting out real bad again.  It threw a Park Neutral
safety switch code.  Put a new one in.  It ran
normal for about 40 miles, then started cutting out
again, randomly. We replaced the fuel filter & my
husband drained some of the diesel to make sure
there wasn't a problem there.   A couple months
ago we put in a new tranny, new injectors.  After
the cutting out issue continued, he replaced the
park neutral safety switch again on the off chance
it was fouled.  He also put a new throttle actuator
in, replaced low speed sensor wire plug, put new
batteries in and cleaned/checked cables (as there
seems to be talk of bad battery/cable connection
causing issues).  On each of these last
replacements, it ran fine for about 30-40 Mike's,
then back to the same cutting.  It hasn't thrown
any other codes (turning the key on, off, on, off,
on).  Also had it hooked up to Smarty Jr and had it
scanned by a friend who has a sophisticated unit.  
It shows good connection to PCM. Possible PCM
needs replaced as it's not throwing any codes,
except for that park neutral safety switch.  Chris
thing is, on the shift indicator, the little digital
square that shows what gear it is in, flashes off
and on.  When it does this, the truck cuts out.  Any
ideas?