I had a SCCA caged Ghia, and I'm still dabbling in VWs. Contact Gex about the transaxle limitations. Not familiar with your 13B, but I've swapped engines where they weren't intended to be. You already know this won't be like the v8-v8 where you make simple new mounts and reroute a hose. Your VW engine is not mounted in the usual sense, it only hangs on the transaxle. So you will need some kind of frame to support a different engine, and you need to somehow tie that to the frameless body you have, which of course means to integrate it with the cage construction. You probably know all that tin is there to prevent air flow from top to bottom except over the heads and barrels, and you won't need any of it with your water-cooled engine, so you can clear it out to make space. Radiator and oil cooling most likely need to be up front where you have air pressure and can reasonably expect flow through. My Renault Dauphine had the radiator back there in front of the engine, but it had side intakes on the body and a lot of research I'm sure to insure enough cooling for the 22hp. You might find some way to use fans, but be real sure you're exiting to a lower pressure area, which usually doesn't include the back of the car. How to proceed depends on restrictions of the class you plan to run (body mods).
When engine system and cooling system locations etc are sufficiently foreign to the body, I like to do a body swap. I've built from scratch too, and much prefer to adapt an existing system rather than scrounge and fab forever. Instead of having to reinvent everything but the wheel, you just have to make simple body mounts and adapt existing things to fit the new envelope. This easy plan probably doesn't square with your new trans on hand and possible lack of donor car attached to the engine you want, and maybe class rules. And maybe dogged personal preference, a trait I admire in members of this forum when it comes to weird combinations.
I realize there's no help in this reply, but it's a conversation. I've got tons of DBHVW from the 70s and 80s. I don't recall any rotary swaps, but I wasn't looking for them either. I'll peruse in my spare time and see what I find. I know there were v8 swaps, so there will surely be something showing radiator installations. Use Google, v8 VW rat rods are showing up these days, you might find something of value re cooling.
Step 1, know which class you plan to run and get very familiar with limitations on body mods. Not just outer shape, find everything about body mods including ducting, venting, clearance, whatever. Everything about this swap is going to hinge on that.