Half time pinion
Hi John,Wish i had a half time pinoin,must be a new mod or something.

I´ve had the same problem on my twin,caused by not tightening E 80 up enough,noticed"the noise" after 500 miles or so.
You mention that it was necessary to make a 5 thou oversized E81.On mine,the key wore,and not the keyway/s(the key being much softer).I fitted a new key,and everything was tight on the mainshaft again.Maybe worth closer investigation methinks.
As you´ve correctly deduced yourself,the flywheel boss (timing side) is almost certainly worn,as nothing else in the line of gubbins on the timing side mainshaft is softer than the flywheel boss,and nothing else can account for the increased play/extra thread/s now showing past E80.
As long as the primary side(PD7) is still F.T,crankshaft alignment will not be an issue.
You´ve got two problems.
1)Swarf (relatively small particles,probably all in the UFM by now,so out of harms way

)
2)A slightly misaligned half time pinion (ET94 & ET92 are still running within there rings/tracks,as the rollers are shorter than the rings are wide (OP31-uninteresting as long as it´s roughly in the middle of the plunger).
I shimmed mine back out flush with the large idler (but then i´m probably an anal retentive,and just wanted all me timing gears running flush).
Shim between ET49 & ET94, or ET94 &OP31 it doesn´t really matter(if you´re lucky,you can get OP31 through the ring from ET94 and so shim between OP31 & ET92).
I can´t quite recall where i shimmed,but there were issues with slot/s in the shim for key/s/way/s,and/or clearance issues with the oil pump plunger when using a large dia shim.
Haven´t had any problems (with this job at least,

)for over six years.
commonsense prevails.
Tip: When tightening ET80 OR PD7 (PD7/2 in my case)
1)Use loctite,fresh,or at least in-date(amazing how many people buy a big bottle of the stuff,don´t realize that its got a shelf life,and keep it in service for 20 odd years.)
2)I use a specially formed (corners rounded off to fit the teeth,and short enough not to touch the primary chain)piece of square aluminium bar,placed between the engine and clutch sprockets(copied from andy everett at the northwest german rally in 2001).
With steadily applied pressure(don´t bounce/jerk or hammer)tighten to F.T (or untill yer shoulders pop)(i use a 40cm long ratchet handle)(ask me for a conversion to inches,i dare ya).With this method,i´ve never stripped a thread,broken a tooth off a sprocket,or bent anything.
P.s If your shaped like Garth,and youré tightening up the halftime E80 with this method,try not to twist the flywheels

,theres a good chap.
Question,"Why did i have this problem in the first place??"
I couldn´t be bothered to remove the primary cover,clutch,other associated gubbins in order to use my "specially formed(corners rounded off to fit the teeth,and short enough so as not to touch the primary chain ,copied from andy everett at the 2001 west german rally) piece of square aluminium bar"!!!.
Lesson learned methinks.