First, thanks to all for the helpful comments and suggestions.  The driveshaft bolts were new ones of the correct length for my '72 R75/5 with the use of lockwashers, and the driveshaft is centered in the tube.   As per Wobbly, the chatter happens only during clutch engagement but DOES go away once fully in gear, and maybe the clutch just needs some break-in.  I did intentionally drag the clutch with the brakes on for a couple of 10 second intervals, and that seems to have helped a little (but maybe wishful thinking).

At this point I am pretty well convinced that the bad gear-like clatter noises I'm getting during clutch engagement are a result of clutch chatter (and thankfully not something worse like a xm suddenly gone bad).  Now for some more assembly background: I did not realize that the clutch pack is a balanced assembly and I never marked original orientations at disassembly, nor were there any pre-existing marks that I noticed.  The engine, while it runs nicely, does seem to have more vibration at idle than it used to.  So, with that error admitted, my plan is to disassemble again (as per D.Elkow suggestion) and send the clutch pack to Southland Clutch for refurbishment (there was some wear and minor scoring on the compression and pressure plates which I initially didn't think was excessive) and hopefully for balancing.  This whole process will likely take several weeks, but I will be sure to update you when complete.

Lastly, one of the interweb resources (Brook Reams '77 R100RS project) explains a procedure to check and correct the run-out of the clutch pack.  Has anyone else done this or familiar the need to do so?

Its been a nasty wet windy nor'easter day here today, perfect for working on the R75/5 down in my shop.  I got the bike disassembled back down to the clutch pack in a record (for me) 3 hrs.  (Practice makes perfect ;-).

I believe I found some serious issues that may have, hopefully, been the cause of the clutch chatter and gear clattering noise.  See pics.  First, the clutch plate was only contacting the compression ring on about the outer 1/4" periphery, thus my compression plate must be quite dished.  Second, and kind of scary, is that there appears to be some kind of, I'll call, microcracks in the compression plate!  These definitely catch the finger nail when run across them!  Anyone ever hear of anything like this before?!?

My recommendation to any other newbies out there is if your clutch plate is bad enough to replace, don't cheap-out by re-using the pressure plate and compression ring, replace them.  Or if there appears to be sufficient meat, at least have Southland Clutch re-machine them.  In my case, they're worn enough to probably warrant replacement, which is what I'm going to do.

When I get the new clutch parts reassembled and the bike re-tested, I'll update this post with the outcome.  I'm optimistic.

Looks like I can only add one file at a time?   Here's pic of cracks.

So, I tore the bike back down to the clutch and installed a new pressure plate and compression ring.  Voila - clutch chattering / gear clattering noises gone.  Smooth shifting.  Besides being worn in general, the diameter of the wear pattern on the old compression ring was somewhat smaller than the diameter of the new clutch plate - another reason that initial wear on the new clutch plate only appeared on the outer edge.  It may have eventually worn in to mate with the old pressure plate and compression ring but I think it was best to replace those parts and avoid any possible collateral damage from the chattering.

That new compression ring (cast) sure is a lot heftier than the original (wrought), about a half pound heavier.  Kind of contrary to those that would lighten their flywheel.  Also doesn't help with my (lack of) balancing condition. 

Glad you found it.

Not sure this could make your noise, but is there any chance your friction disc is in backwards?