I guess I should clarify what I meant by going option 2.
You have fixed dimensions with the drive train your using. Tubing etc can be moved around to make things fit. Certian things take up a certian amount of space. Seats, headroom, etc. it is definetly a whole package, and certian things are just sized the way they are.
Figure out what you want the rig for, what you want it to do, etc. Figure out what your willing to sacrifice to get what you want. No rig can do everything super. Do you want it to be low and super stable on big climbs/sidehills and drops, or do you want belly clearance and height for the mud and boulder fields? Do you need storage room for camping, do you want to go 100mph through the desert and jump off dunes? Do you want to be shoulder to shoulder with your pasenger or do you want a little bit of elbow room.
Figure out what you want for a wheelbase, belly pan height, roof height etc. Make sure you give yourself enough head height etc.
Take a look at other chassis people are selling a lot of them give measurments, that will give you a rough idea if what your thinking is in the right ballpark #'s wise.
A generic sized chassis to fit anybodies combo of parts is a compromise of different things to make a multiple # of combos of parts fit.
here is a good example of starting with your drivetrain...
http://pirate4x4.com/forum/showthread.php?t=610875&highlight=lovell
a very nice looking rig and its winning comps if you care about that stuff.