Sounds great! Here are some plans.... (tee hee)

[ame="http://www.youtube.com/watch?v=YZ_xyh4ehNo&feature=related"]YouTube- Gigabyte Mainboard Factory[/ame]

I've been in a board manufacturer before, and this is the method that they used:
Screenprint solder paste (stainless screens), 3D vision system to check for paste registration (and volume), pick and place machine(including pick, scan to check orientation, rotate to correct, and place)(as in the video above), then another vision system to confirm, and finally the reflow oven. You could obviously skip the pre and post paste vision systems (what I saw was pretty high volume).
If the boards are small, consider processing them joined together then do a final op (punch, or route) to separate into individual boards.

It sounds fun! I'm looking forward hearing all about it!