Getting very frustrated with mis fire

Sorry I posted this on tdi 101 but I figured this might help to put it on the mk5 page too. So my 2006 Jetta tdi was shaking at idle and just not running very well. So I took it into a German auto repair shop near me that specializes in VW, Audi and Porsche. They found that the cam had went out and the #1 injector wasn't working correctly. Now this was strange to me considering that I had had the cam replaced 50,000 miles ago and the injectors had been rebuilt 30,000 miles ago. Well it turns out the guy who had replaced my cam put the bearings in wrong or something but bottom line it wasn't getting the oil it needed. So I bought a stage 2 cam from kerma tdi and had the shop replace it. Then they flip flopped the #1 and #2 injectors and the mis fire followed to cylinder 2. So I took the injector out and sent it to the same place I had it rebuilt and they said it had been contaminated with bad fuel. So they cleaned it and made sure it was to spec and then I put it back in. The car still idles like poop and runs shakey until about 2,000 rpm and then it takes off like it's running fine. I'm just at a loss for what it might be so I was wondering if anyone out there has had a similar problem

Are you certain it is actually misfiring? Does it have any DTCs? What are the smooth idle compensation numbers?

A wiped out DMF will feel exactly like a dead cylinder at low RPMs when they get really bad.

Yeah it had a p0301 which is misfire cylinder 1. I haven't checked the diagnostics since I got the car back but I would assume it says cylinder 2 is misfiring now since they switched the injectors. And it has a p0674 which is the #4 glowplug. And if dmf means dual mass flywheel, I don't think it's that since that also went out about 3,000 miles ago and had been replaced. Also the EGR was replaced at the same time as the dmf. The cars got 268,000 miles on it so I expect to be replacing a lot of stuff now but it's getting to be too expensive lol and also what are smooth idle compensation numbers? Do I need a vag-com to see those?

What oil are you using?

I use Castrol edge sae 5w-40 full synthetic but I'm not sure what the shop just put in it when they changed the cam just now

VCDS will show smooth idle compensation, yes. It may also show more DTCs that you may not have seen if you were just using a generic OBD2 scan tool.

I have had two places who said they could rebuild PD injectors screw them up so bad I had to replace them. I would check their credentials or find someone else with some known success with them, and send them all four of yours for a proper evaluation.

Sometimes the injector harness can have a bad connection in the head, too.

I think this is a pretty good place that rebuilds them. It's dwb llc out of Boise Idaho. But I had also replaced the harness thinking it was that but it didn't change anything

So I ran my obd2 scanner again and the fault codes are a p0101 mass air flow sensor and misfire on cylinder 2 and a code for glow plug #3. I was wondering if that had anything to do with each other since the #3 glow plug is on the #2 cylinder? And also I replaced the injector wiring harness so I was also wondering if maybe the connection on the injector itself could be bad?

Sounds to me like you have a bad injector.

If you had a #1 cyl misfire, and you moved that injector to cyl #2, and now you have #2 cyl misfire, seems pretty obvious.

Well then where would be a good place to send it to get it checked out? Because I assumed the place I sent it would have been a pretty good place given that they specialize in tdi injectors

I would contact that place and ask them. They may be happy to take another look at it for you.