The unit you are looking at replaces the stock muffler on a 2 into 1 exhaust system, so the inlet to the muffler is probably at least 2" ID. I would guess more likely 2-1/2" ID. You should be able to adapt it to the stock header without too much trouble. A quick inquirey with the vendor might get you a concrete answer about the ID.
Thunderheader exhaust systems work really great on Harleys. However, they are mighty loud. Since you intend to use it on a single cylinder, it will most likely be even louder. If noise is a concern, this might not be the muffler for you. If you don't care about noise, have at it.
If you are running the stock carburetor, you shouldn't have too much trouble tuning. The thundercone muffler will most certainly flow a lot better than the stock muffler, but it won't be anything like a straight pipe. Exhaust reversion shouldn't be much of an issue. The stock carb is very forgiving. Just make sure you have a good selection of main and pilot jets and some #4 washers (or equivalent) to adjust the needle in the slide.
Of utmost importance, if you install the Thundercone muffler, make sure you do a post with lots of pictures and an evaluation of how it works. Gotta share.