I did the same thing to my Carat a few years ago. I'll try and find some pictures for you tomorrow. A tip to line up the luggage rack brackets that worked well for me is to put double sided foam tape to the bottom of the brackets with them lightly screwed into the luggage rack. Make sure you put the seal on so it lines up right. With a helper lay it in place and press down. Loosen the screws and the brackets should be set. If you haven't already measure the rear hinge holes 4 times before you drill. They are the least forgiving. To bolt the rear hinges down I used flat steel stock  and drilled and tapped holes to match the hinge holes. It helps support the weight of the poptop better. To brace the lifting arms bend out a short length of angle iron to the roof contour. The sheet metal will bend if you don't. I used welting (sp?) to finish the hole in the roof with the headliner. Best of luck with your project. When you start cutting the big hole you may be overcome with the feeling that you ruined a perfectly good Vanagon just measure alot and it should work out just fine. 

I'm so slow, and I procrastinate, but today I drilled the tin top for =
the pop top hinges (and backing plate), marked out the cut lines and the =
canvas securing track on the roof, and cut the headliner a bit to pull =
the insulation. I think I'll be cutting the big hole tomorrow.

I must have measured everything at least 4 times, but I am still uneasy =
:)

pics of today's work here (and some pics of my home made "jack bombay" =
pop top assist strut assemblies)

http://shufti.wordpress.com/

alistair