captain do you have a pic of your headers from the front? my left pipe looks nothing like yours, its has a flat bend to it at the bottom...yours are very close and neat looking..
ps. your 88 should NOT vibrate...are lugging it too much? maybe go up the rev range more and report back
ever since putting back tthe twin headers and oem muffler the bike is even more smooth as there is not extreme thumping like before...
exhausts make a big difference in perceived thumpiness if you will
If I lug my xr really low it will rattle and shake
but never at the bars, so thats worrisome you have that...I get it in the frame and foopegs but never enough to NUMB me.
also our 88 bikes are nice with vibes because they have a twin gear balancer shaft...that is spring loaded unlike otheryear xr6...this is to help with the slamming effect of the crank when accelerating hard or downshifting...
other year xrs have a nice whine to them and slappiness if you will until warmed up because of this(different cam chain as well on 86 and down models, they were bigger)
hope you get it sorted
nice 88 btw! once again