I didn't use any rtv and it was ok for me 10k miles later.
The MSA gasket is fine, but I think I actually used a felpro one when I did it bcause I didn't like the material of the msa gasket.
Gasket side doesn't matter, I believe it's curved just because of the sheet they print it out from.
Torque is in the fsm, but I tightened as much as I could with a 3/8's ratchet or a short wrench, just don't overdue it.
Leaving the heat shield will help, but I never used one, I had coated headers with an N42 shaved intake above and never had any problems in my ZX.
I had to use the 6-2-1 headers, and I brought the y pipe to my muffler shop and they shortened it all there before I installed them. The headers I had tucked up above the frame rails, so they didn't scrape. My 260z with 6-1 headers did scrape at the rear of the exhaust system because whoever made it sucked, the headers were never a problem.