Hi there. I'm in the Seattle area and received my Mk4 this last Sunday.
Mistakes I've made:
1. Ordered the windshield wiper. I'm not going to be driving in the rain and can keep / use a detachable manual one should it come to it. Space behind the dash and above the passenger footbox is at a premium and there isn't room for the wiper motor, defroster, and glovebox. Should you really want an electric wiper, there are better electric ones out there.
2. Ordered the vinyl dash. It seemed convenient at the time but I don't like the cut-outs as they are. Moving them and filling in the precut holes would both be a pain and look terrible. I was also doing diamond stitch and my wife was planning on sewing the dash cover in the same pattern.
The biggest mistake might actually be yet to present itself. I was going to buy a transmission from Monster but wound up switching to Gear Star. I made sure with Monster to have a 31-spline count input shaft but after checking with Gear Star, it appears I didn't share that with them. It doesn't say on my BOM and now I'll be counting the splines this weekend. If it is off, then I'm having to purchase another drive shaft (~$450 w/ shipping.)
I ordered the Wilwood brakes but was told that they are overkill for nearly everything but track. Even on the track the standard brakes are usually sufficient. Since I plan on taking the car to the track, I'm not too worked up with this.
I could have deleted some of the parking brake components as well and saved a little. I plan on using an electric one from EStopp.
I stuck with the single-adjustable Koni shocks. Even the track guys said that unless it was going to be a track only car, not to bother with the double-adjustable.
I'll let you know if I messed up on the drive shaft.