Shifter won't shift

Real simple. Get a manual, and split it. It's not rocket science, and don't pry on the cases to get them apart. I use a steering wheel puller to split mine, it works. If you don't already have the flywheel off, buy the proper puller, they're cheap.

I know but do you know what may be causing this?

I have had this problem 20 years ago on a RM. Which is the same set up as in your picture. Where the shifter shaft locates with the shift drum, you can see x2 spring loaded shift pawls. My shift pawls got worn on the edges and it just locked solid. I'm not saying this is the case with your bike, but I would check it before splitting the motor.

www.karlzracing.com

Splitting cases is pretty cheap. Youll need some gaskets and silicone sealant(yamabond). Might as well replace all the bearings since youre in there. Id say under $100 if you do it all yourself. Might get the crank rebuilt too if its seen a ton of hours.

I would suggest you broke a gear. It can also break a bearing. These issues can even cause case damage.
The best bet is to do a tear down and find the problem.
The cost will depend on what is broken. It can run anywhere from a few hundred dollars including broken parts and new top end plus gaskets to around $1000 if you put in all new bearings and crank.
Your best investment will be for a service manual.

Paw Paw