Those dont appear to be threaded, are they?  

It looks like those are mating points to be used with collar inserts.  Maybe Im wrong.

They are just for alignment I believe, so no torque on them or stress really.  Looks like someone used them for a pivot point to pry with a screwdriver or something.

To be honest, I don’t even know if the damage I’m seeing on my motor is conducive with what would be seen from a lack of torque limiter. Can anyone confirm that this is the common problem from this year group engine? It seems like too much torque from “kickback” would put a metric nuts-ton of stress on those mount points. I’m just wondering if I JBweld and remove stock to get it as close to original as possible... would there still be too much pressure on it even if I upgrade the gears?

Verslagen1, do you have a picture or drawing of what you said about pressing a steel sleeve over the boss? Is that in addition to JBweld or in lieu of?

  I'd take Dave up on his generous offer, rather than a repair that might fail over time, but I'd be concerned with what caused that damage in the first place. Converting to the anti kickback gear would prevent this , but there's other things that may have caused it , be sure that you use the proper rotor and MATCHING  ignition TDI module (the magnets for the pickup coil are in different places on the 4 and 5 speeds )  , so the timing is correct,  running the carb slightly rich will help prevent kickback ,as well as shifting the bike to neutral and pulling the choke out just before hitting the kill switch , this makes the fuel/air mix in the exhaust header so rich that there isn't enough oxygen to support combustion ,so that kickback cannot occur.

If you are looking at replacing the bottom end anyway, consider swapping in the later engine that already has the torque limiter installed. You only need to swap your rotor onto the newer engine and bolt it in.

Check the marketplace section, I think SoC still has a 5 speed listed there that has minor head damage from an accident, and your head is a bolt on for it.