Just upgraded the alternator and starter, checked fluids, replaced the battery with a new AGM and lubed the input spline.
All is well for a couple of short day rides and then the horrible noise started in the tranny.
Checked and rechecked everything, found nothing obvious.
Searched around and found a post on
www.boxerworks.com that matched my symptoms.
Horrible vibration and noise on acceleration at the beginning of a shift change. No noise on down-shift or from the engine when the cluth is pulled. So...
Input shaft shock absorber nibs are sheared 
Good news: Economically it may make more sense to buy a good used tranny instead. The good news is still bad, just better than the really bad...
So now I am searching, watching and hoping a good tranny pops up.
Got a couple of watches on Ebay and some classified sites.
If anyone has a good ~50k mile tranny they need to find a good home for...
Of course I will trade a bag full of coins and promise to take care of it, feed it some good synthetic and moly the splines regularly.