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Are you a member on the Vortex? if not, that is the first thing I would suggest. There are so many things that you can do with a swap, depending on if you have a whole donor parts vehicle so you can get the wiring harness and the ECM, or if you are going to swap the 16v head onto the 8v block, etc.
Try starting at this thread, and then follow some of the links in that thread to individual member threads where they document their swaps. It will give you a lot of ideas.
I'm pretty jealous, I live in the rust belt in Minnesota now and even if I could get one, would not want to subject a MKII to this weather! i had an '89 in Seattle that was pretty fun while I had it...
Either transmission will bolt up.
If it doesn't have a timing belt on it, I hope it hasn't bent the valves or something serious like that. i don't know if you plan on tearing it down to build it completely.
The water pump should bolt right up- most of the differences are in the head, and in the fuel injectio system
Your fuel system is determined by the ECM that you are using, and by what you have in the vehicle. CIS is pretty simple- it regulates the fuel flow to the injectors by how much air is going through the airbox, as a lift plate operates in the throat of the system. The fuel distributor sits on top of the airbox because of this. Digifant, which came right after, always had some problems.
There is a book that has been out for quite a while by Greg Raven, great book to have if you are doing a swap, or even just like watercooled VWs in general- http://www.gregraven.org/hotwater/
I would also make sure to sign up on VWVortex if you haven't already, and frequent their forums. There are so many ways to do a swap, plenty of them right in their own way, and maybe some things you didn't think of trying. People with a 16v head on an 8v block, etc...
Dodges can be pretty easy (at least the truck engines) but VW is pretty simple. Timing is easy to set up, all of the parts are bulletproof, if you torque things right you won't have head gasket failures or anything, run good coolant!