Since I had to take the manifolds off, and I know that a couple of the thin gaskets blew out, I thought I'd run a file over the flanges while I was cleaning them up, just see how flat they were.
They weren't. Which is amazing, considering this is 1/2" plate that those tubes are welded to, but stainless loves to warp and pull with heat (As I have had Great Fun™ with, on the ongoing work project. See below) I filed them until there was a good solid ring around both ports.
Then I applied a healthy saucing of high-performance exhaust ketchup, and nailed 'em back on, taking care to install them in such a way as they could pull in nice and square.
With the exhaust ketchup setting, I moved on to tackling the intake manifold. It looked like my best bet was to put the throttle-body on an angle, and notch the portion where it just hits the cab.
I've also decided to fit the throttle-body in a different orientation, to try and squeak just a little more space; and hopefully by all those changes combined, I should now have the room to get this manifold in. Not yet checked to see whether or not those fuel lines have clearance to the exhaust manifold, but I'm hopeful that I can tweak those if needs be.
The ongoing work project:
It is absolutely amazing just how much stainless will warp. c.c