Christian K - lot of activity on here so hope you're still checking in. If your tractor seems to run fine for about 1/2 hour then I can't see any problem with the carb. If your tractor is still at the shop I'd definitely pick it up and get away from there as fast as you can.
Now, on your plug, I would definitely re-gap it to at least .025 or even .030. I believe IH called out .025 and Kohler .035 (if you study all the Kohler literature they jump all around but .025 is correct for the AQS engine in our applications).
You also mentioned using Marvel MO - are you putting it in the gas and if so how much??? To much is like trying to burn oil in a gasoline engine.
Now, about the weak spark, are you getting that by looking at the spark on the plug, or looking at the points? The spark at the points is notorious for looking weak when it really isn't. My suspicion of your problem goes directly to valves as you first thought. If you dis-assembled the carb and cleaned it I'd think you have the skills to check the gap on your valves lifters and adjust them as necessary. You will need a feeler gauge, a breather gasket kit and the Service Manual. I recommend the IH CC Engine Service Manual so you don't get all confused using a Kohler Manual. For the Quiet Line series IH CC published a Chassis Service Manual that covers everything except the engine, and they published an Engine Service Manual (I believe both manuals are for the 1x8/9 and the Quiet Line so you may have to look in the Manuals section under both Models/series). I don't know if Charlie has the Engine Manual in the Manuals thread on here, but hope so, since it only covers the engines used in the IH CC units (not all the applications shown in the Kohler manual).
I'm gonna bet you'll find your valve clearances out of adjustment. If you do check and adjust them and still have a problem, my next step would be to remove the head and have a look at the valves and carbon build up. You might want to do this anyway if you have never de-carboned the head and piston. It's supposed to be done every 500 hours of operation - and carbon will KILL your KOHLER if you don't.
Good luck and keep us posted of your progress.
Jason S - besides the A frame you'll need the trip springs as well and maybe the lower bracket since I can't see a pin on it where the springs would connect. You can probably find most or all the parts in used condition - but they most likely will total more than the cost of a complete snow blade for a Narrow Frame CC like your Model 100. (I've seen the sub-frames sell for $50-75 each, the A-frame by itself for $50-75, and a pair of springs for $50-60).
For what it's worth - I'm not sure your QA42 snow thrower will bolt up to your 100 either. The 100 was prior to the "Quick Attach" (QA series) latch and I believe only 2 of the holes in the mounting bracket for the QA will line up, and the QA will have 2 pins pointing inward that will conflict with the 100. Unless the QA has been modified already you'll have to do some modifications of your own - but I believe it can be done.
Joe Becker - thanks for your service to our country. We don't get many active duty personnel on this Forum but I'm hopefully someone within the 2 or 3 states around Arkansas can help direct you. I see you're not far from Little Rock which ain't terrible far from some places in MO and TN. We have some members in both those states and maybe some even in AR. Hopefully they'll see your request and help out here.
You definitely need a small engine machine shop that is familiar with and done several Kohler K-series engines. It sounds to me like you're gonna need the block bored and the crankshaft ground AND hopefully both are within the spec limits to have this done. In my view the crank has the most critical tolerance, so please don't just try to get by.
I wonder if Jerry Bliler is still checking in on here. He was very knowledgeable on the internals of these engines. I don't think he was a machinist but worked many of them over and probably knows a machine ship someplace in MO that specializes in these Kohler K-series blocks.