I think I figured out the problem on my bike (and maybe on ranchomice??). I've never had the copper crush ring gaskets in either the front or rear header. I never had a leak there, so didn't worry about buying and adding them since I had a good seal. But I just added those copper rings last night, and adding them realigned the pipes just enough so that now the other connections fit perfectly. So make sure you have good copper rings installed if you're having fitment issues . . .

Also, I'd bought two of those "foil" gaskets from bike bandit over the last year, and they both arrived to me in poor condition. At the time, I thought that's just what they looked like, so didn't know any better. But the ones I bought from Ron Ayers just now arrived in perfect condition (no cracking or fraying). That made installing them much easier since they weren't falling apart before I even touched them. They basically slid right on, and I was able to get a tight seal without destroying them.

I used the jack method that geekonamotorcycle described above to raise the main pipe onto the downpipe, and hold it there while I clamped everything down. That helped a lot, but just be careful not to over-jack it and drop the bike.