If it ran good and your spark plugs looked good I wouldn't mess with it. Just put it back together let it warm up and cool down a few times and run it, but I would check your plugs after you run it and make sure you're not lean
If you have the carb flipped up sidedown, you see where the float bowls pivot. There is a little tang off of the float assembly that pushes on the needle to close the seat when the carb is full of fuel. All you have to do is adjust that tang to whatever height you need to achieve.
You can either do that or get a set of cut domes that allow the piston to come above deck. I've seen it done both ways and IMO the cut domes work a little better. Here's a place that sells exactly what you're talking about doing.
http://www.vitosperformance.com/atv_parts/...&cat=200&page=1
Just from what I'm looking @ in your pics I'd say the main clutch hub nut came off. Remove all 6 of the bolts that hold your pressure plate on and take a look, I bet that nut came off. If it did come off you will have to put it back on and get a new lock tab for the nut.
If the deck surface or the cool head is not flat, you can have issues. There's really no way to know how much damage it's done until you pop te head. Where are you located?
You should check the harness, also you might want to pop off your flywheel and shake it if it rattles the magnets could be damaged and could contribute to your problem.
I have the same problem, just notch the plastic to get it off then take a cut off wheel and and cut around the plastic to get the bolt out, Then jb weld a new nut in
The v 3's come with a down sized plastic (stuffer) that constricts the air flow with the bigger carbs. The bigger stuffer allows more intake flow (like the v 2's)