So I am new to DIY car installations and I have a question or two.

I have the dash mount kit and I have taken out the factory HU, but I have found that the alpine adapters for my Volkswagen don't seem to fit what I need for the Scion. Do I need to buy another wiring harness? If that is the solution, do I have to make any alterations that anyone knows about? Thanks.

not much alterations..

buy new wiring harness kit, and wire it to your aftermarket deck. thus it can plug right into your car without cutting any of the wiring in the car itself.

Toyota and VW adapters aren't universal. Looks like you'll need to purchase a Toyota harness like Squall said.

and after that, its all pretty much plug-n-play. a very easy install.

thanks, I got the harness and installed the deck and accompanying ipod controller clean and easy. However, I just noticed today that now the automatic feature on the windows and moonroof ceases to work. The windows still open, but no longer will they open automatically like they used to. Has anyone run into this problem before?

check your manual on how to reset it.