On my first CMC build I deleted the VW rubber seal and used 6 or 8 tubes of clear Silicon caulk (GE brand, I think), laying down a generously think (3/8"-1/2" thick) double bead along the entire pan-to-body seam. There are two spots , 1 front and 1 rear and right over the central tunnel) that will require that you shoot a bunch more caulk in there after you set the body on the pan - just a really poor design job on the body metal frame allowing a huge gap at the top of the tunnel.
It's OK to let the caulk set up to semi-firm......The body will just squish it out and seal everything up.
Remember that you'll have to skew the rear of the body left or right a bit to center it over the rear wheels or it'll be a little off forever. Doing the all-silicon approach seemed to work about as well as anyone else on here, and I went back later, after identifying a few leaking areas at the back and re-caulked into the seam to stop them up. Once THAT was done, I shot a couple of cans of aerosol rubberized undercoat into the seam just to make sure. No leaks since.
On my next build I used a new VW pan gasket, cut to fit the shorter pan. That went a little easier, but I still gooped the hell out of it with silicon caulk before putting everything together. That had a tendency to move around a bit as the body frame was being mated to the pan and was a bit frustrating, but it was OK in the end. After it was all set up and cured I shot the same rubberized undercoat along all of the seams to really seal it up.
I never finished that car (Merklin did and re-sold it) but it looked pretty well sealed when done.
I like the silicon caulk because it has a working temp range beyond our seasonal temperature swings so it stays pliable no matter what.