So, I stopped in to the dealer on my way to work today to talk about this grinding issue. Turns out it IS in fact a known issue with some of the 1000's and CFMoto (Canada at least) will automatically approve the job under warranty, no questions asked. The guys at the dealer were already somewhat aware of my particular machine and weren't really that surprised that it is still doing it. Apparently the shift forks on the affected models are weak and bend/wear just enough that they have trouble grabbing the gears, it's not the actual gears themselves grinding, but the tabs on the fork fingers. Parts include new forks, primary gear(s), and a few other things. Says I'm not gonna hurt anything running it for now, although I'll still continue to be careful with it.
Best part is, they're gonna order in all the parts required to do the job first, and THEN book it in for a couple days to do the repair so I'm not without it for more than 2 or 3 days. I've actually been impressed as hell with how well this particular dealer has treated me since day one (Yard Gear in Fredericton NB). I'm pumped that it was in fact a known issue, and that it will be fixed properly without losing half the summer with it! Thanks you guys for all your help and tips, it is always appreciated!