Alright, so I've had this miss that's sorta there and sorta isn't. It's more prevalent when it's cold out and is bad enough in the morning to make the truck jerk and irritate me. On the freeway in 5th I can feel it just steadily (when it's fully warmed up) when under load. I'm not really sure what the issue is. I tend to think it's probably a poorly atomizing injector as when it does this it tends to smoke, but in the back of my mind compression is always a concern. I don't have a diesel compression tester either.
I'd just like to know what's going on with this thing because it sort of helps me to determine what I'm going to do with the truck. I have a 1.6 TD longblock which I can rebuild, but it has wavy cylinders so it's going to need a new set of pistons and I don't like the idea of investing ~$600 in that right now.
This thing is going to end up turbocharged one way or another so I'm thinking of just using the one that's in it for now and seeing how that goes. I bought a pyrometer and a boost gauge so tuning shouldn't be a problem. I just don't know if I want to swap everything out to find the engine is screwed up...
So those are my ramblings... Anyone have a similar experience with their engine?
yea my car misses like crazy! But only on a cold startup. Lots of blue smoke for about a minute. Then it goes away

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I'm hoping its just a bad glow plug, because then I don't really care and will change it sometime when its warm out. Would sticky rings have anything to do with bad startups/bad compression?
I'm dealing with the same problem with my jetta, but only when it is cold and when it is hot. When it's cold it misses like crazy, and on a hot summer day when idling it also misses. Engine is rebuilt, new injectors, new glowplugs. I am about to replace the injection pump. Hope that works.
hmmm... when my engine is cold it has more power than when it is fully warmed up. doesn't misfire though
hmmm... when my engine is cold it has more power than when it is fully warmed up. doesn't misfire though 
two reasons for that: 1. the air coming into the engine is hotter when it is fully warmed up than when it is cold. Hotter air is less dense, so you get less oxygen per unit of air put into the engine. Intercoolers help a lot with this problem.
2nd reason: worn injection pumps give less fuel pressure when they are hot than when they are cold. Reason is that metal expands when it is heated, so any clearances that are too large as a result of wear and tear, get even larger when the metal heats up. I find my Jetta runs the worst and has the least power on hot summer days, because the injection pump has 400,000+ km on it and is a piece of sh*t. Fortunately, I have ordered a new pump. Should get it next week and put it in hopefully within a few days if I don't encounter any problems. Should run sweet after that.
thnx chrissev! I think I will just continue to annoy all the drivers who are behind me if it means getting a new pump. As for intercooler though I might just have to try that
My IPs seals leak when it is really cold out. I noticed that the throttle return spring area gets moist.
I also get a rough idle when it's so cold out that the fuel starts to gel. I haven't had a roughness when moving so when this starts to happen I go straight home.
Steve
You can perform a cylinder cutout test when the engine is missing. Crack open each injection line at the injector, one at a time with a rag over it. There should be a noticeable change in RPMs. If there's no or very little change, you've found the weak cylinder. You'd then want to check the valvetrain and pressure test the cylinder. If all is ok, replace the injector.