CATCRD wrote:
In my mind, the bottom end is the last, and most expensive thing to check. Maybe your timing belt just skipped a few teeth and broke some rockers. That can cause noise, rough running, no power and backfiring out the intake. Was the timing belt replaced at 100,000 mi? Was the timing belt tensioner replaced at that time? It will be easy and cheap for a mechanic to check cam/crank timing or pull the timing cover to look at the belt. That's where I'd have them start.
Respectfully, checking the cam/crank timing alignment using the pins as gages is relatively easy, and if the alignment is off then you have a good place to start looking. CATCRD is right in that idle regulation problems are typically caused by faults in fuel or air supply; this can be valves, injectors, turbo, timing, etc.; the CRD is notorious for being unforgiving on timing belt PM intervals, and there have been a number of posts that described symptoms similar to yours that were in fact issues with the timing.
That said, looking at the belt on this engine is NOT easy, and NOT cheap, at least as far as I am concerned,
and would not give you much more information than the pin alignment check would; if the alignment is now off, then you know what happened, and are looking at new rockers and timing belt components. After I did the easy check of cam/crank alignment, if that shows as OK, then I would take Geordi's advice and check the lower end by dropping the pan. That's my thought, and it is worth what you paid for it. 
Regardless of the designer's intent, I suspect that ruining a few sets of rockers has to be hard on the lower end, and may have contributed to Geordi's two lower end failures, so if you have indeed suffered collapse of the rockers due to TB failure, if it were my engine, I would do just what Geordi suggests and pay somebody to look at the rod bearing clearances and bolts.
As far as who to have do the work, I would look for a good independent TDI mechanic, and pay him and some good mechanic from the forum, like Sir Sam, for a couple of hours of consult time prior to letting them get their hooks into your Jeep.