Good luck. I was going to do the Doepfer DIY but went eurocrack instead. Might still do it eventually when my bank account recovers since I like a nice project myself.
As far as compatability, afaik all modular formats are compatible with each other. The only issue you'll run into is going from 1/4" to 1/8" jacks or banana to 1/8", etc, but that can all be rectified with the proper converters or diy cables.
I suppose the best way would be to look at where you'll expand from the Doepfer DIY and go from there. If you're going to expand into eurorack, maybe keep it to 1/8" jacks. If you're planning to go into something more DIY friendly (like Frac), figure out what connector you like best and you can standardize that way. I've never tried them but many people seem to really like banana jacks over anything else for the feel and easy stackability for multing.
As far as DIY modules, it seems like you'll have the most options in 5U or Frac Rack. There are a few for Euro but not nearly as much yet.
edit: I should add, there's a great modular forum that also has a DIY section you should check out: http://muffwiggler.com/