I'm assuming the pic of the headers is showing the shorty headers which you had before with a solid flange, and the long tube headers which have the individual flanges. I have similar long tubes and I have learned over the years is to thread the bolts into the rear holes of the flanges first, and then do the front holes. I use Remflex gaskets that don't have the hooked holes, so it's a bit more difficult. On the driver's side, I start threading bolts into the rear holes on the #5 and #8 exhaust ports, and then do #6 and #7. Like mentioned previous, I thread just enough to have the bolt started and then go to the next one. Once the rears are done, then I start working on the fronts. Once they're all started in, I tighten one flange at a time.
I've started a blog about my car and adventures: http://65mustangfun.blogspot.com/
1965 Fastback, 289, Toploader 4 Speed, owned by me since June 1980. Originally a C-code with a C-4. 5R09C16****