It's been 2-3 years since the Bosch pump we have in there was installed. I just got off the phone with the shop that did it, they warranty 12k or 1 year, they don't have records, computer crash, blah blah. They wouldn't even tell me who they got the pump from so I can avoid that same supplier. After this call, I'll go out of my way to never do business with them again.
We're now deciding to pay the $950 or so for a rebuild from boraparts, or triplet, or to pay the $1500 for a VW pump from the dealer. Either way, I think at this point we're sure we need a new pump. Maybe even send the injectors out, if the pump has been knocking like that for a while, there could be all sorts of tiny metal bits floating around in the system.
Thanks again to everyone who helped out. Hopefully after a bit of saving we'll have a new pump and we can at least get her started. Then the real fun begins in diagnosing all the other little problems this neglected little car has got.