Bummer about losing the space for the heater. But it sounds like you have a great perspective on personalizing the engineering to fit your needs rather than everyone elses. I'm really interested to see how your 2.5" LCD "rearview mirrors" work out.
I've been thinking about your 4" floor lift design -- what are you going to do about the pedals? If you take the stock pedals and mount them in the stock location, you won't have any room to push them 'cause they'll be on the floor. If you mount them higher, you'll have to wrap them around the steering. If you mount them in the stock location, but cut the arms to better fit the space, you'll lose leverage. Interesting puzzle.
You raised the question "... how high should the car be off the ground with a flat underside?". I was looking at it from the perspective of how would the suspension need to be set up to handle road conditions well -- In the article I read at
http://www.whiteline.com.au/articles/RH_SwiftGtia.htm, lthey came up with the best combination of handling and ride quality with progressive springs on the front and linear springs in the rear - with ride height of 320mm (12.6") front and 305mm (12") rear - measured from the center of the wheel to the guard. The author of the article goes on to say "It is possible to lower ... more however, after many tests ... have found that further lowering does not allow sufficient travel for the bumps to be soaked up, causes shock absorber damage and adversely affects the handling."
Part of your answer may hinge on how flat the road is that you're planning to drive on? You might be better off with a little higher ground clearance and some flexable air dam material on the front and sides, then beating up your smooth belly pan on a rough road.
Have you had your weigh in yet, to see how your weight reduction program is going?
You're work is an inspiration. Can't wait to see it on the road. Keep up the good work.