The BEW is one of my favorite engines because it is so RELIABLE. Good maintenance is the key.
The first big mistake is thinking a timing belt lasts 100,000 miles. It actually can, but not many make the real reason for changing the belt... it's 100k OR 5 years; whichever comes first. So, based on time, your engine is due for it's third timing belt job. Forget the miles. 2 years ago, I changed an original timing belt on a 2003 Beetle with 27,000 miles. The belt would have blown off in 100 miles, if attempted. The cogs on the belt were cracked and falling off.
The cam is a known issue on these cars. We designed a true hydraulic cam profile, altered the cam bearings, cam and rocker shaft bolts, and much prefer to set up the best oil for improved cam longevity. Although we have a list of the 505.01 VW certified oils allowed for our cam, we have our preference, and that is Schaeffer's 9000 5-40. I think we have developed a cult following with that oil.
The cam, which can be as short-lived as 70,000 miles in the BRM, tends to last longer in the BEW, with 10 less hp. However, the aftermarket cams last a much shorter life expectancy than the OEM and our modified cam outlasts the OEM. So, we suggest a peek at the cam. Remove the EGR valve, the timing belt cover and the valve cover. Look for galling on the base circle and a sharp edge on the cam lobe. Either problem means excessive cam wear.
The other maintenance that is nearly completely avoided is brake fluid flush. That should be done every two years, but getting it done in 5 years, stresses some people.
It can be done with a helper pumping the brakes, while you shout,"UP... DOWN!", as you open and close the bleeder valves on the brake cylinders or a pressure bleeder attached to the reservoir makes the job quick and easy. Start at rear right, then left, front right and left, you are done with each brake cylinder when clean fluid comes out.
The injectors are incredibly long-lasting as long as they get good, clean #2 diesel. Occasionally, we might purge the injectors with LiquiMoly Diesel Purge, used straight. Clamp off the lines past the fuel filter and for the inlet, install a small in-line fuel filter going to the 'IN' side of the tandem pump and let the 'OUT' line go back into the can.
We use two cans, letting the engine completely cool down before using the second can. Run the engine at idle for 1/2 hr uses about the whole can. The idle balance numbers are always improved in VCDS by using a diesel purge.
Check the gear oil level in the transmission. Our contention is there are two ways to ruin a 02J transmission. 1. See how much torque you can put into it leaving the line.
2. Let the tranny run out of gear oil by not inspecting your output shaft seals. The leaking seals are the most common way to blow out the transmission synchros and bearings.
If you pull the 17mm allen plug and oil comes out on flat ground, it's full. if the oil is brown, muddy or has flecks of gold in it, change the gear oil.
The OEM gear oil is a GL-4. It's the right stuff, for sure. DON'T buy gear oils that say compatible for GL-4/ GL5. That is not possible. GL-5 is meant for steel syncros. The sulfur and phosphates are a much higher level in the GL-5. When the parts get hot, a black coating of the sulfur/ phosphate becomes a sacrificial element, that at the higher levels, peels the brass molecules off your synchronizer rings. The classic synchromesh gear oils or Redline MTL are good choices.
Rear shocks are worn, but this time. If you find the tires getting 'saw-tooth' tread, 'alligator back' and make noise at speed, it's not the tires, it's the shocks. Replace not only the shock but the shock tower with bushing to restore ride and lower road noise. Same with subframe mounts. They get hard and transfer a lot of road noise.
That's a very good start..
If you need any additional advice or information, feel free to call.