I have 20K miles on my SPF and like it a lot. I wouldn't say there's any one "best" car out there-depends on your criteria-but to me, the Ford IRS with the upper and lower wishbones and the extra room in the cockpit were big pluses; also the availability of the car as a turn key minus. Like probably everybody else, I play the "What if" game from time to time and I keep coming back to SPF, at least for the way I use the car. I'm more interested in having a dependable, (relatively) easy to live with sports car that looks pretty much like a Cobra, than an identical replica, although I do understand the guys who prefer more authenticity.
My frame rails are about 4" to 4-1/2" from the ground, so, yeah, the bellhousing must be at about 3-1/2". I did scrape the bellhousing once, at very low speed, pulling into a driveway on a speed bump which was hidden by a shadow. I do angle up sharp driveway approaches but you get used to looking out for stuff like that. Also dodging the dead coons and 'possums in the middle of your lane...
At this point in time, I think the Cobra replica market is so competetive that any of the currently available kits or rollers can be built into a very nice car if you take enough time, lavish enough attention and spend enough money. Do SPF's have issues? Sure: Every now and then when I'm working on my car, I find something that makes me go "Jeez...now why did they do THAT?", but I'd guess you would find that on any car you didn't build yourself.
Even now, as a Cobra owner of four years, I could be happy with any of several Cobras but I still feel the car I have fills my current needs best.
Good luck,
Lowell