I'm on my second 2000 Jetta TDI. Had to get another after the first was rear ended.
The ALH engine is nigh bulletproof.
There's actually two good forums for TDI owners (TDIclub, and myturbodiesel), and many more general VW based info at VW vortex.
I'm probably due for a partial suspension refresh. Some work was done, changing some of the bushings front and rear, ball joints etc. But the front struts look like they are getting tired after 16 years, and the rubber mounts for those up above have probably been squished down a might bit.
My intake I haven't checked on recently, but the EGR is bypassed on this one. Cleaning it out when it does have the stock EGR, and then not babying the engine at low revs for months goes a way to preventing buildup. For the most part, that issue with the EGR was only in the earlier years of your car's life, because the Ultra low sulfur diesel (ULSD) switch happened in North America about a decade ago, and put the fuel to the same specs that Europe had when the car was designed and introduced.
One issue to mind, as I'd had to change it on both TDIs -- mind your steering rack. If the power steering pump squeals at all, get the proper, expensive fluid and top it up... if it repeats and you see leaks near either bellow on the steering rack, you have a new rack to swap in on the horizon. The earlier the better, or like any power steering failure on any car, you risk causing damage to the pump as well.
This second TDI of mine, didn't shift as well as the first, and at the end of last month, I've lost 5th gear. I thought it was a shifter issue, and tried adjusting and repairing... but it's actually bits in the transmission to service.
Having the bottom engine cover and side skirts keeps the engine cleaner. If you're missing yours, the stock sideskirts are easy enough to get again, but the cover is better replaced with a metal skidplate. The oil pans on that generation of TDI are cast aluminum, and the 1.9L engine sits about an inch lower than the gasoline engines do. (This why both the skidplate and having refreshed front suspension bits are important - to keep that oil pan from scraping or striking)
Most of my fixes to the car have been sorta-kinda returning the car more to stock condition. Or substituting other model parts in (mostly for the interior). I'm lucky, in a way, because Canada had the Mk4 carried over as the City Jetta until 2009, so I've managed to swap parts in from 6-8 year newer cars than mine.
Work done:
* Replaced carpet with a 2006 City Jetta. The pegs for the stock mats changed, but you can get replacement clips for the mats to match.
* Swapped out Wolfsburg seats, front and back, to get rid of the mismatched set of seats the previous owner had in place. Seats in the Mk4s are all interchangable.
* Added a "tuning" box that affects fueling - it's a glorified Evry mod. But it gives lots of pep to the car... at the cost of some city mileage.
* Replaced the stolen aftermarket blingy-ricey radio installed by the previous owner with a Blaupunkt unit, that has the same ISO plugs as the early model Mk4s, so there was no rewiring mess to do while we were in the midst moving appartments!
* Found the Blaupunkt too blingy, the lighting does not match the rest of the car well enough, and I slowly acquired a stock stereo and CD player (early Mk4s had them as two single-DIN units).
* Learned to disassemble seats in the living room, to my wife's chagrin, and added lumbar support from a set of leather seats to my Wolfsburg seats. The seats are universal for parts, so any thing another seat has can be hobbled into yours. Reskinning seats, as well, is relatively easy, but some tools are required.
* Changed the back half of the center console to a late model year Mk4 console, that has cupholders beside the parking brake, instead of hanging cups above the shifter and stereo.
* Bought a cheap leather jacket, and learnt to sew my own gaiter and shift knob out of leather, to replace a very tired and smelling-of-cigars one I pilfered from a wrecked Turbo Beetle.
* Swapped out the stock 4 spoke, buttonless steering wheel for a... Mk6 Jetta's buttonless 3 spoke steering wheel. Just to be different.
I've got to get some delayed because of winter maintenance out of the way.
* Replace trim from sound deadening work, which was semi-successful (IMO, refreshing the suspension should be done first)
* Test, acquire tools, and refresh the throw out bearing on a transmission I picked up to replace mine. Got it cheap, but it engages all gears properly, and is filthy.
* Replace the missing bottom engine cover with an aluminum skidplate that was already purchased
Less critical, but interior work still needs doing.
* Fix the heated Wolfsburg seats I put into the car, in case I actually experience a COLD winter.
* R&R Headliner, recovering it while it's out. Haven't decided on what material and what colour to go with, so that's waiting for warm weather and a fabric purchase.
* Will probably make a leather cover for the rim of my steering wheel, because "black" Interior parts in the Mk6 are not the same shade of black in the Mk4.
* May consider re-upholstering the A/B/C pillar trim, after I decide on the headliner.
* Timing belt change is on the horizon. I have 295,000 km on my car, last belt was changed at 220,000 km. This was two owners ago, so I do not know if they used the original belt kit the last change, or the higher mileage 100k miles/160k km belt kit that the 2002 and up models had stock.
More research/testing/parts required to...
* Hard-wire my dash cam, so it has a dedicated USB plug.
* Splice in a second 12V cigarette lighter plug off the center console
* Change out LEDs on the interior (minus the door lock light, it's molded into the trim). I was contemplating a switch from red to blue, but it's SO hard to match the blue on the instrument cluster to get the right intensity and shade. Probably going to opt for white LEDs. Need to sort out proper resistors for the LEDs so I don't have 7 levels of brightness from the various switches and backlights.
* Change out LEDs on the instrument cluster. Still have to buy the surface mount PLCC-2 LEDs for this. Changing out the blue for another colour (white?) requires about 22-25 LEDs to be swapped.
* See if during the LED swap, I can dim the WAY too bright high-beam indicator light, so it's less bright and won't wreck my night vision while driving.
* Want to persue making a small carputer as CD "changer" with the OEM stereo, so that I have the ability to play mp3 or FLAC files instead of burning audio CDs like it's ... 2000 again. Others have made code for this, have some parts and both an Arduino and a RasPi that reserved for this project. Need time to investigate code and how to interface with the car.
And... there's future projects, for when I have a house, and am free to use a garage bay as a shop.
Looking forward to gearing up for the transmission swap. Without 5th, driving on the highway will be both more costly, and much louder. And with the tools I need for the swap, I'll be well prepared for the next timing belt change.