An interesting side note to this is that with the dynamic components in SketchUp 7 you can assign variables of all sorts to your joinery (and timbers, pretty much anything). When you use the 'report' feature you can break out the joinery from the timber (and sips, trim, floors, etc.) If you were crafty enough you could write statements into your joints - so a tenon of a certain size would be equal to X $$$ and a tenon of a different size would be equal to $$ (this would have to include the mortise and housing + the tenon).
Of course, this is probably overkill for the first 5 frames or so - but once you build it, anytime you pull a joint from your library - that data is embedded in it (or to simplify, you could just assign a value - like 'J2' for medium difficulty, and 'J3' for harder, etc. or by type... - then do a 'gut' check on your output and throw a number at it).
But, its all theory until you understand what you can cut in an hour, per man, then figure out your shop rate, per man, per hour. And break it down from there. And don't forget to add your burdens to it - rent, profit margin, benefits, taxes, rainy day fund, donut fund, medical, etc. etc.
Spreadsheets. Mmmm.
