I bought the late great Mr. Patches at 230,800 miles. He is rusting now at 278,5xx... I went ahead and say 279k.
The automatic is going to give up again at some point. If you do fluid and filter changes it can probably see 180k of use. I'd be prepared (ie start sourcing) a 5-speed swap if you intend to keep this car. You'll also see a MASSIVE increase in fuel economy... I went from 44/52 city/highway in my manual to 36/44 with the automatic. The automatic sucks up fuel, is slow, and frankly I hate it. With a passion. I'm swapping Patches manual into Phoenix in January I hate the automatic THAT much.
Now my bit on transmissions aside. You'll want to probably be ready for a Fuel Shut off Solenoid O-ring. The car may rev high at startup and act like it's losing power, no turbo. It's air in the fuel lines from the leaking O-ring. $3 part. I don't have a number.. just keep this in mind for down the line.
With a 99 you'll be replacing window regulators, interior plastics, and headlights long before you'll pop the engine apart for anything more than a valve cover gasket or perhaps, maybe, a headgasket. These engines are insanely overbuilt (they debuted in 1988 as an Audi model).
We have several members with 300k or over 300k miles on their vehicles; TDIclub I've seen some pushing 600 and 700,000 miles. They do stand the test of time.
Automatics, I should note, use a 11mm fuel pump where manuals use a 10mm. If the pump leaks kill the auto and swap manual; a manual pump is gonna be $900 to rebuild or about $1100 new... automatic pumps are rarer and I've seen $3k price tags for them. If performance is your goal... it's the pump you want (that's why I bought an automatic, this car will put 160 to the front wheels when I'm done with it).
I think this is the smartest thing you'll buy. You should do it, and just be prepared for stupid little things, it'll always start and drive (hopefully... it is an automatic) but it won't get 50mpg as configured. In fact if you get 40 in the city on an automatic you're doing better than most.
GO for it!
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Phoenix: 2003 Uni-Red New Beetle GLS TDI 140k former-automatic with a 1998 TDI Manual Transmission swap.
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