First - the shim - he wants you to move the entire flywheel - with no regard for anything else, like starter engagement - he's just concerned about the clutch ...
Not quite how I would be doing it.
Second - clutch adjustment - I could be wrong - but - whilst you can shift the clutch lever/arm on the splines, I doubt it was intended to be used as an adjustment - look closely and see if you find "alignment marks" - two dots, one on the lever/arm, one on the shaft - if you do, there is only one correct position, with the two dots adjacent to one another.
Regarding your machinist - you might be surprised by what a skilled machinist can do with a lathe - the first time I had a cylinder head resurfaced it was done on a lathe, and I went from blowing out head gaskets every few weeks to never changing another gasket on that engine. If the lathe is large enough to hold the flywheel (and that takes a decent sized lathe), and the machinist knows his stuff, I wouldn't be too bothered about the fact that he's using a lathe.
What struck me as odd earlier is that the machinist wanted to remove 0.025 in, it sounded like a lot - I've never had a flywheel that needed to have that much removed - is it badly scored or are you just doing a routine resurface because you're replacing the clutch?
I see where you are going with the flywheel and starter. I can understand that.
To tell if there are alignment marks on the pedal shaft I'd have to remove it.. I can't get enough of a look to tell but I think I have it close enough for working right. It was fine before I removed the transmission. I had good pedal feel.
This is just a routine maintenance for a new clutch, I'm removing the 1.8 and putting in a 2.3 engine and upgrading to a better clutch because of the increase in potential power. There is minimal scoring on the flywheel and it just shows what looks to me like normal wear.
Just doing what is supposed to be done when installing a new clutch. New pressure plate, new clutch disc, with a resurfaced flywheel.
At least this is always how i was taught by my mechanic Dad that you do it all and skipping any of it is asking for trouble.
I've spent some additional time researching this and have come to the following conclusions.
There are essentially 4 types of clutch actuation (at least what I have found)
Full mechanical
Pedal to linkage (levers, rods) to lever actuated bearing (Not related to Suzuki)
Cable - mechanical
Pedal to cable to lever actuated bearing ( Samurai Sidekick except Sport) have this
Hydraulic mechanical
Pedal to hydraulic line to lever actuated bearing (Sidekick Sport)
Full Hydraulic
Pedal to hydraulic line to fluid actuated bearing (Not related to Suzuki)
The clutch mechanism on my Sidekick sport is Hydraulic mechanical Pedal to hydraulic cylinder that actuates the mechanical lever inside the bell housing. Instead of cable, hydraulic fluid moves the lever.
I believe that the reason the machinist was concerned about shimming the flywheel is for a Full Hydraulic setup where adjustment is probably not as easy.
So there should be no reason to 'shim' the flywheel for this setup as there should be sufficient adjustment in the 'plunger' on the hydraulic cylinder.
Which is probably the reason why I can't find any shims.
So I think I am set. I just need to go back and explain this, When I talked to the machinist we only discussed hydraulic clutch and he probably meant full hydraulic and thus his concerns about shimming.
If i'm missing the mark.. somebody help me out.