Actually you may want to call Griggs Racing. They were one of the first to do this swap and make a tubular K-member for that purpose. Also check out (if you haven't all ready
) Stangparts. Its a good place to look for those hard to find little, but needed, parts for cheap. Like master cylinders, lines, hoses, wires, ect.
As far as the Cobra vs. Mark VIII DOHC: Go with a Cobra block and crank if possible. The Cobra has a stronger 6 bolt block (although I have seen some hi-po Mark VIII blocked cars) and the Cobra crank is much better. Its made of forged steel, while the Mark VIII is made of iron, all be it a higher grade then the GTs. The Cobra rods are also bigger/stronger then the Mark VIII, although they are both made out of powdered, cracked, steel. The Cobra short block can sustain 450 rwhp for extended periods, but you have to be very careful with the tuning.
Oh yeah. The Mark VIII heads are the same as the 96-98 Cobras, but with less agressive cams. The Mark VIII varies, but is a similiar design to the Cobra, but not as free flowing.
Buying a wrecked Cobra would be good idea.
Links:
http://www.griggsracing.com/
http://www.stangparts.com/
BTW: Stangparts has a couple complete Cobra engines as well as a couple Cobra cranks which will fit in a Mark VIII block.
Keep us updated. My brother and law is considering doing a similar swap for his 85 GT.