ATV engines, since they have an integral transmission, are rather complex systems. However, if you're handy with mechanical kinds of things and aren't afraid to get your hands dirty, there is a lot that one can do in terms of overhaul and repair of these engines. I would start with the OEM service manual for that particular machine. (The factory produces a much better manual than the after-market publishers do/ good illustrations beat the best photographs too.)
The factory manual will also clue you in on specific tools you might need to remove clutches, flywheel, or other parts specific to that machine.
It might also be worth viewing parts fiche screens online if you have some idea about what might need replacing, worst-case scenario anyway.
If that is not an option for you, a service dealer for your particular machine should be able to give you a labor estimate for doing a full-open engine overhaul. I would expect you'll be looking at upwards of $1000 labor for a full teardown.
I've spoken to one place that works on all recreation toys and they told me it would be "thousands" to repair.
I found rebuilt engines on ebay but they are almost 3 grand just for the engine.
I'm debating if I should just sell it as parts salvage machine. The rest of it is in good to excellent condition and its the NRA edition with full camo.
If I went that route, what would be a reasonable price to ask for it?