I like the use of the magnetic gauge pins.
Some interesting discussion in some of the replies :
https://www.facebook.com/100053249992034/posts/darkhorse-motor-company-leaders-in-the-industry-of-harley-davidson-performance-p/1068226558295667/

rollies replaced primary seals a couple years ago not sure if main crank seal was done ,i replaced that seal 3000 km ago, looking at the old sleeve/race the marks where the seal sat they look even not sure if the seal is oe just stabbing in dark,

found the problem, put dye in engine went for a 85km ride after couple days didn't think gone far enough but checked anyway dye in all three compartments ,checked crank runout at compensator outer edge .016 thou (.4mm) checked  lock nut washer the same, marked the spots runout in the same spot.i know some will say check at crank but to far out to go any further if it was close id go further. I believe this all stems from head on  accident 11000 km ago complete front end replacement, have reopened insurance claim waiting for assor to visit

well insurance says wear and tear looks like I'm going to rebuild the old girl i have a pinion shaft runout tool on the way ill check properly to see how much the shaft is actually out and decide weather to replace or repair flywheel assembly , seems the only ones available are s&s looking at 3 grand i cannot find a cheaper brand than that,why cheaper you say 1 budget tight ,2 im not a boy racer give it a bit of stick occasionally and do mostly touring im 69 done 85000 km so i think ill be doing well to do another 85000 on her  ,anyone out here got a take out flywheel sitting around let me know,surely there was a lot of upgrades from when these bikes were new if anyone interested ill keep you posted

I've seen take out engines for sale for less than the S&S crank, obviously they are an unknown. 

i know someone who used to do flywheel straitening in their workshop and still has the gear we are going to have a crack at it and see how it turns out 

bought a dial indicator 2 thou runout on pinion shaft is this ok or straighten fly wheel needed

.002" is pretty good, think the " Harley " allowable limit is. 012", that's way too much, I wouldn't pull it in half for 2 thou. 

when it was flywheel i at least had a direction, now not sure,ill strip the primary and see what i find

Trying to think this through, the dye went from engine to primary to gearbox, you are positive of that, taking that as yes. 

(it's odd because you said at one point the primary was low and the excess in the gearbox refilled the primary to the correct level.)this bit here oil migrated to gearbox primary found low of oil no external leaks after dealership service geabox not checked at this time not thinking migration problem  all oils changed and refilled road bike 3000 km rechecked at this time checked all levels geabox up primary down, readjust levels dye put in engine, my next move dismantle primary and check main seal

after 85 km no noticeable difference in levels but dye in all compartments, definitely 200 ml short in primary and 200 ml over in gearbox after 3000 km stuff all on engine down that i recall .new breathers in top, all breather passages clear including gearbox breather, no external leaks,im suspecting compensator spring wear a result of low oil,im led to believe that the seal behind clutch can assist with migration from primary to gearbox. im hoping when i dismantle primary tomorrow i might see a path with dye.

No it's not normal

so maybe bearing tight in spots

The stator and rotor (magnets ) can cause an unusual feel if rotating by hand .
Hard to call without having hands on to feel it.

there is a slight tight spot on primary chain i have a auto tensioner think on re install will go back to manual that could play a part in tight spot as well ,i gotta dismantle primary anyway so no need to panic just yet until apart currently looking at .003 runout on pinion shaft,just so i got this right, when cam chest empty, primary striped crankshaft should spin freely ?,i have to wait until tuesday i cannot crack compesator nut and need to borrow rattle gun from someone who ows me a favor

You have piston and barrels on this motor right?

The friction from those alone will stop it from ''moving freely" 

It will move, but will still require force to overcome that. 

thanks for that tip i was thinking along those lines

Resistance yeah but jittery na