Don't worry about that frame to pipe dimension, different brands, in my experience, line up differently depending on the manufacturing angle at the head. I've had three sets of header pipes and none of them aligned the same way. My current set - can't remember the brand but I got them from OB - are the best of the ones I've had. OTOH, I've never had a set that couldn't fit in the mufflers. If that's a problem, one way to do it is to unbolt the mufflers, install the new headpipes very loosely, slide the muffs/clamp onto the pipes, align the muff mounts and LOOSELY attach the mounting bolts (just attach the nuts enough to keep them from falling off). Then tighten down the head pipes, followed by the muffler mounting nuts, followed by the muffler to headpipe clamp. There will be sufficient "flex" in the muffler shock mounts to accommodate any mis-alignment.