Steve,
Not trying to jump on you at all but two things jumped out at me from your picture. First, I agree with Pat that directly above the axle is not a good place for that fuel filter, regardless how much clearance you think you have to spare. An unexpected trip through a ditch or over a curb at speed might change a bumpy ride into an inferno - not a happy thought. Second, your shocks seem to be leaned forward a bunch! I know that someone posted a neat link about how the angles affect response, but absent that I found this little table that seems to be about right:
Attachment 56233
In your discussion on tacking your motor mounts, do you have your engine and tranny bolted together as a unit so you can set your drive line angle and deal with all clearances at once? I would think it would be a lot easier to triangulate supports with the pieces joined, allowing you to establish not only the motor mount locations, but the tranny cross member, too, all with the chassis at ride height?