I used some JB Weld and some flashing on the hatch. It's been curing all night, and in a couple hours I'll get a chance to see how well it's taken. I figured I had nothing to lose at this point, and it'd be nice to milk a couple more years out of it. If its sticking ok I'll see about doing some more. I did see a door on CL for $50, but looking at the manual it looks like a pain to pull. Ebay has fenders for $100 apiece, that is starting to look tempting.
Should add, the only time the car has been under a roof is for a couple of overnight stays at a garage. I think it's held up well, for 9 NH winters, a minimum of washes, and some known problem areas.
I did get in contact with someone who has VCDS, and will likely troubleshoot the engine in a couple of weeks.