don't need any bolts or dowel pins
get the rear main, get the pilot bearing. the pilot bearing is what goes into the very end of the crankshaft that the very tip of the input shaft from the trans seats into.
Very interesting debate about clutches. I, too am not a very big spec fan. All the shops I have been too highly recommend against them also, but because of the chattering issues, they won't sell them for this reason as well.
Normally, I would highly recommend against the king cobra, especially for your higher output, however, the disc you mention seems better than the standard king cobra, as the standard KC disc is all organic from what I understand. Do you know anything more about this disc?? sounds pretty good.
keep the stock length clutch fork. If you're nervous about your old one, buyfordracing.com (diversified) sells an oem style clutch fork brand new with a brand new oem non adjustable cable for $39 or so, can't beat that deal.