Update: got the car back today, and seems to be running normally. Here's what it said on the receipt thing (typos are sic):
Found code P0087 per TSB 01-10-11 Removed fuel filter and found metal shavings checked for fuel contamination non found. Per tech line due to metal shavings recommend replacing the fuel system. Replaced fuel lines, fuel injector, fuel filter, fuel pump, cleared faults and set basic settings road tested vehicle and it working as designed
And the stuff replaced:
1x 03L-130-321 - Pipe
1x 03L-130-301 - Pipe
1x 03L-130-089 - Fuel Distr
1x 5N0-130-307-J - Pipe
1x 1K0-127-400-F - Fuelfilter
1x 03L-130-235-K - Pipe
4x 03L-130-277-A - Injectunit
1x 03L-130-301-R - Pipe
1x 03L-130-301-B - Pipe
1x 1K0-201-060-GP - Tank
1x 5N0-906-129-B - Fuel pump
1x 03L-130-755-A - Pump
1x 03L-130-301-C - Pipe
1x 1K0-919-050-J - Fuel unit
1x 1K0-253-141-M - Clamp
The service rep said she would try to get the old pump part number but the tech who took it out had already gone home, I'll try to follow up tomorrow. Good service, all things considering, Stevens Creek VW in San Jose. No connection to them, would recommend for dealer needs.