There's no endplay spec, of which I am aware. The play isn't in the bearings, it's how they fit inside the cases. I agree with the others who have already replied in this thread; there's normally/typically a substantial amount of endplay, just as you've described. FYI, the new-gen motors have virtually none of this...the clutch-side bearing is pressed onto the crank, the RH case half heated to install the bearing - which seats solidly inside the case half. If anything, bearing clearances expand with heat. That includes the outer races, which tend to fit the case halves more snugly (while the inner/outer "grip" on the ball bearings loosens). Between the typical 0.009-0.015" rod-to-counterwieght clearance of most crank assemblies and (by comparison) acreage between the small and of the rod and the piston, it all works well enough. If there were an inherent issue, we'd have know about it decades ago.
So, if you want to use a shim to tighten the clearances, it is possible. The question, imho, is one of practicality. Excessive endplay, could have more than one cause. A ~0.005" shim is not only going to be thin, it's going to be narrow and not all that easy to work with. It will also be easily overlooked, the next time the engine is disassembled. Who would notice, let alone remember, an unusual custom part like this? It'd probably be better to shim the clutch side bearing, on the crank. The problem is that then you have a crankshaft that may not be usable in another set of cases, unless the shim is removed...somewhat of a hassle and re-e-e-e-e-e-eally easy to overlook. It'd be more accurate to almost impossible to notice. If you know, with 100% certainty, that the excess clearance is a result of the case half/halves being incorrectly machined, the next step is figuring out which half...if it's not both. This is where impracticality rears its head. How do you accurately make that determination? For most owners, the logical method would be to source another RH case half. If that "cures" the issue, may as well just use that part and call it a success. OTOH, the LH case half is the one with the SN and for most, that will be an issue. Only way to correct that would be welding-up, then re-machining the bearing bore...a high-precision job that must be done perfectly, the first time, and it won't be cheap. The actual machining will be the "easy" part. The setup requires a seasoned pro who cares greatly about the work.
My suggestion is to take a close look at the crank & case halves. Is there a ton of sideplay (more than ~0.018") at the big end of the rod? Any radial runout? Take a look at the small end. Does the wrist pin fit loosely enough that you can feel it rocking inside the rod? How about the bearing seats...any "witness marks" signs of the bearings dancing around, causing wear? If all of those parts check out, in acceptable condition, well..."if it ain't broke..." An extra 0.002" due to a narrower assembled crankshaft length shouldn't be an issue. FWIW, the trailbikes engine parts...including their stroker cranks...have been very reliable for a number of years now.
The one thing that would motivate me to have a shim made would be flywheel-to-stator contact. That'd also dictate where the shim goes, the clutch side.