You definitely need to take care of those fuel leaks. I'd start with the injector hoses as those are easy to do. The delivery valve o-rings, assuming that's the source of the IP leak, most likely wouldn't cause this sort of a problem but should be addressed eventually. However if it is the shutoff valve or its seal that's leaking (the black box on the side of the IP) then it could very well be causing or at least contributing to this problem.

I don't think it's the K40 relay because in my experience a bad one would cause sudden engine shutdowns instead of rough running. I don't know about the MAF sensor as my car doesn't have one, but I believe yours does and if it is bad it could be causing the K40 relay to mismanage the fuel delivery. First, though, I'd take care of the leaks. I assume your fuel filters are fairly fresh and your prefilter o-ring seals well, otherwise they could be the problem too.

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2004 VW Jetta TDI (manual)

Past MB's: '96 E300D, '83 240D, '82 300D, '87 300D, '87 420SEL