Jason,
The autostick or 'slushbox' tranny-equipped VW doesn't seem to have a good reputation among those who have driven them. I had the opportunity to test drive one about 10 years ago, and I didn't think it was anything I would want.
As I stated in a previous post, I would seriously consider replacing your
69's chassis with a standard transmission-equipped one. If you are planning on replacing floorpans anyway, finding such a chassis will be a lot easier than trying to find replacement parts and competant repair data for the 'slushbox' gear.
Removing the body is not difficult, and is the preferred way to get at the floor pans for replacement. This will also give you vastly improved access to the heater channels and other rust-prone areas. If the floor pans are badly rusted, chances are the heater channels are, too. Get a big screwdriver and mercilessly probe any areas that look suspect.
At the very least, pulling the body from your your 69 will be a good learning experience, and give you a better idea of what you have. You may decide that a different car would be a better starting point. The '68 VW that I paid $1800 for in 1997 looked fairly good on the outside, but had had lots of body work done over the years and turned out to be a real rat's nest of rust. It took 2 1/2 years to set everything right, and it is my current daily driver, but in retrospect I could have done a lot better starting with a more solid car.
Good luck!
Al Adams