I know EXACTLY what is causing this: in 2008, Honda hired a new vendor to make these pipes for us. (I'm not complaining, exactly, as we can now GET new pipes for a change...) This new vendor has shifted the little collar at the footpeg in the #2 pipe about 3mm in their jig. This causes both left side pipes to misalign.
I took my old #2 pipes and measured the collar, then ground off the offset with my trusty Dremel tool and a cutoff wheel (heavy-duty type: this is hard chrome) to match on the inside length. Then I added a shim washer beteen the pipes, where the collar is too short, to make up the difference. It brought them close enough together (side-to-side when the footpeg is tightened) to install the little rubber coupling at the back again.
Even so, the #2 pipe required a new copper donut seal in the head and #1 required a used one, to get the curve spacing to work out right. The #2 pipe is the issue: it is not curved just exactly right either, making it effectively a little longer between the head and the footpeg.
The #2 pipe in the HM341 series has always been the one that wears out first. The chain lube plugs the drain holes near the pipe-muffler joint, and they rust out right there. Because this pipe sells about 2-to-1 over the others, I suspect the original molds for this one have recently been rebuilt or replaced, causing this situation. And, none too accurately.
In the end with these pipes, it's probably best to fit them up loosely at the head first, with the rubber coupling tied in at the back and the footpeg bolted finger-tight, to discover where the misalignment is, and what to do with it. It's been about 8 months since I put them on my K2, but I think I cut 3mm off the inside of the collar, added a 1/8" thick washer between the two pipes at the footpeg, having to grind a matching angle on the offending collar to let the pipes sit together properly, and I may have 2 copper gaskets in the head at #2 exhaust port (I've forgotten that part: this was four 750s ago...).
On and off over the years, Honda has had this issue with all of the 4-pipe bikes when they contract out the parts to a new vendor. When the SOHC Fours were younger and the Honda shops worked on them, the feedback to Honda was quick and the problems got resolved pretty early. I suspect that if this info could get back to Honda somehow, they would fix the problem: they may not even know about it because shops don't work on these bikes anymore.
