Runs rough

That is classic limp mode. Is it an automatic or manual gearbox?

There is a writeup at the top of the forum here: http://www.myturbodiesel.com/1000q_how_to/multi/limpmodetdi.htm It describes exactly what you are feeling and how to fix it. Your car shuts down power to protect itself against some malfunction. It's probably a sticky n75 boost controlling valve or a broken vacuum line. Since it only happens sometimes, it's not too bad but it'll be hard to spot the broken line, so just replace all of them.

2nd, because you said that it is fine on restart, this is a big clue that you are experiencing limp mode. It's not the fuel filter because otherwise it would be more constant.

Also check for boost leaks. You could have popped an intake hose loose. If you look around the engine bay, look for loose clamps, split couplers, etc. If you can't see any, you can try the boost leak test metioned at the top of the forum. You fill the intake tract with compressed air and see if it holds pressure. If not, then something is leaking. If it isn't even pressurizing at all, if it's just hissing away immediately, then you have a big leak.

That happened to me, classic limp mode. Look through the how to article on it. If it's really bad, it could be a detached hose.

It is an automatic.

I don't think it's a transmission issue since you said it runs fine sometimes. You could get the car scanned for codes. These cars tend to get bad air flow sensors. If a vacuum line was broken or a hose popped off, then these could make the car run poorly. Take it to the auto parts store, places like autozone will scan the car for free, see if there are any error codes.

Thanks for all your help. It ended up being the timing belt.

Rough Engine

I cannot think that the roughness was due to timing belt. Of course it could be the timing was off caused may be by belt losing a tooth, but very remote.

Dodoma said:

I cannot think that the roughness was due to timing belt. Of course it could be the timing was off caused may be by belt losing a tooth, but very remote.

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It can be the timing belt, I remember reading about someone whose belt slipped. It was right on for the camshaft and crankshaft so no valves went "boom", but the injection pump sprocket slipped. It's rare but it could happen.