3406E missing

Here goes; I have a 97 Pete 379 with a 550hp 5EK and genuine CAT filters. Last September I took it to my local CAT shop because I was noticing a miss, and told them I thought an injector had gone bad.
The shop said it was fine, "no problems".
A month later I took it back again, "it's gotta have a bad injector. It misses and the boost is down to 28lbs"
The shop again said it was fine.
Another month goes by, I take it back. "Fuel mileage is down to 4.9, boost is 28, and it misses. I want new injectors"
This time they say the ECM is "breaking down" and that it's the root of my problems.

So, I ordered a 'Stage 1' box from PDI Diesel (thanks William!)
CAT puts it on, and nothing changes (but it did make 521hp on the dyno)
After a few weeks, I get back to town and complain again, "it has a bad injector"
"Nope, the new ECM is bad" they say. So we swap computers, PDI tests theirs, says its perfect, and it goes back on (another three weeks)

I take it back AGAIN, later that day I get the call, "your injectors on #1 &2 are bad" (really?!)
In go the new injectors (CAT reman), run the rack, new jake springs (since they were off anyways)

NOW she's runnin'! 674hp on the dyno, 36lbs boost, 7.3mpg, one smooth puller!

30 days go by and its missing again! Boost is down to 30/31, 5.7mpg, misses below 1500 including idle.
CAT tested the injectors electronicaly, and said they were "in spec"

What could be going on here?! Help PLEASE!!!

 

Thanks man. I probably should have been pushier, or even gone to another shop, but they weren't about to give me a refund and I wanted them to do the work I already paid for. I still think it's got a bad injector, just because they're rebuilt doesn't mean they're good.

I really credit PDI Diesel too. Their ECM really woke this ol' gal up! In fact, yesterday I pulled the Grapevine into LA at 60mph on the cruise!
I know now that Mr. Haney does similar work, but I was unaware before hand.

 

Good info! It didn't even dawn on me until now, but CAT did have to fix the wiring to a couple of the jake solinoids (three times!). Unfortunately, I have no idea where this bend is, or which connector to look at. Is this something I can take care of, or am I looking at some sort of dealer wiring harness (ECM to valve cover or valve cover to injector)?

 

You'd think they would have been thorough, but we're all human (and I think they were getting sick of me!) I wonder where they plugged in at to to the electrical test on the injectors themselves?