need engine for a 2003 jetta tdi wagon

Have a 2003 jetta tdi wagon with auto tranny. Car has 140,000 miles and was running great when it suddenly lost power and is barely running. A new brain was put in, no change. Then was told it needs a fuel injection pump for $2000. Then after pulling off the valve cover, was told the engine is shot and I need to replace it for $4000. Timing belt was changed about 20,000 miles ago and is still o.k.Car is in nice condition and wife wants to keep it. Where do find a good engine? And what should it cost to buy it and install it?

Sounds like you've already thrown some money at it, consider finding a good mechanic to look it over. Interweb guessing you had an event. Evaluate clylinder head, crankshaft, connecting rods and pistons.
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Take it to 413 Auto in Westfield MA. I think he's the closest guru to you. Replacing the ECU (or "brain") is a flag for me as they rarely fail. And IP failures are rarely sudden, usually there are indicators.

Mike both knows just about everything about these cars, and also has done many engine swaps. He may seem far away, but getting it to him will save you significantly in the long run. I think his contact info is here in the Trusted Mechanics section. If not PM me and I'll provide.

I agree, get it to someone who actually knows what they are looking at, and get an informed opinion and diagnosis.

Yep, find out what's REALLY wrong and get an estimate to repair it or replace it if needed, but put some real thought into dumping a lot of money into a car with a tranny that has a (very) poor history and can cost a bunch to replace or swap to a manual.

Remember that you have a desirable car, even with the 01M.
You very likely do not need a new engine as the bottom end is very robust on it.
There are several scenarios that can have those symptoms so take it to a guru!