Might I suggest, setting up a rolling chassis, and playing with the stance you want:
Just frame, forks, swing arm (no shocks), and wheels.
Use some blocks (wood) of different sizes to set your "stance" up. Once it gets to where its what your lookin for, start checking out whats going on (travel, rake and trail, etc). See if there will be any problems you can identify (like ifd you want drag pipes, but you only have 3" of ground clearance, you may have a problem), and if they can be remedied, or needs to be avoided by doing something else.
Not everyone is born with all the knowledge needed to build an Iron Horse cover bike. Asking questions is good. At least by asking questions, you can get a clue.
Hope that helps, and good luck!