To answer your question I think the adjuster bolts are 5/16ths thread but that really doesn't matter IMO.

What you should do is loosed both of them then reset your belt tension and using the correct tool or it's equivalent make sure your axle is square to your pivot bolts on your frame.

 

Shovels used to eat that lip regular, common causes were loose motor mounts, misalignment issues between the motor, trans and inner primary covers, things get to vibrating that lip goes by by every time. Correct fix is tear down have the lip tig welded and built back up then machined down. I made an arbor to hold the case half in a lathe just for this, repaired several this way. Any decent machines shop should be able to handle it also.

This isn't an option for you get busy checking the above issues and somewhere out there there's a aftermarket gasket just for this problem. Tom84FXST has posted it a few times in the shovelhead section. Whatever you do don't go crazy with big globs of the blue or red silicon as I usually see when this happens and no JB weld isn't going to fix this..........

 

It's easy to machine the case on a lathe with a large faceplate or on a mill with a rotary table. I forget the makers but a couple of outfits sold case repair rings which would also be easy to turn. Since aluminum is unsuitable for such a pathetically thin lip the best fix would be steel with a light press fit and anaerobic adhesive. (Good weldors who can weld old oil-saturated cast aluminum aren't plentiful.) Making another delicate aluminum lip isn't an upgrade.

It's typical on modern aircraft. Gaskets require scraping which produces debris and slows parts replacement. Unfortunately the inner primary covers are not flat nor have they sufficient room. HD got the O-ring right but clinging to the legacy inner primary/case lip mess makes conversion impractical.
If you REALLY want to stop leaks you can use aircraft fuel tank sealant but it's considerably more work to take apart sealed joints. I get my 'B-1/2" fix from Aircraft Spruce and Ebay.

 

So question - information on belt alignment is pathetically thin. Search terms bring up a thousand different results.

I took your advice, undid the belt all the way - put the trans pulley back on and played with the tension on the bike.

I measured the alignment of the center of the axle to the end of the swingarms, and counted the threads past the end of the adjuster nuts. All this has shown me I am within a half a MM of being perfectly even. Is this an acceptable threshold for error?

The current belt and trans pulley alignment has a 1.5-2mm steady gap between the lip of the trans pully and the edge of the belt.

I am waiting for a belt tension gauge to show up to get the final tension on it. My final drive sprocket tool comes in on Friday to tighten that down too.