I’m having a hard time getting the intake manifold and carburetor to seal. I have sanded the ends and replaced the gaskets and o ring. Is there a sealant that will work there or is there an aftermarket replacement available?

Hello and welcome !
Did you flat plane the carb? Thats when you take the carb end and set it on a piece of sandpaper with some oil on it and sand it on a flat surface such as a mirror or something similar. Sometimes over-tightening can warp the flange and cause an air leak.
Got any pictures?

They're not generally prone to leaking there unless there's some severe damage. Is it possible for a photo or video of it running & concentrating on that area. Can you hear it sucking or taking in spray if you spray the area while running. What are the symptoms if they're not that obvious--lean idling etc, choke not doing its job. things like that.

There should be a new gasket on each side of the intake block and a proper oring. Yamaha really over built it to prevent leaks. As was already mentioned...don't over tighten nuts. That will warp the flange and cause other problems too. Check for cracks in parts or otherwise not flat mating surfaces.

Thanks for the responses. I did flat plane the manifold but not the carburetor and......I cracked the manifold. I put a flat edge in the carb flange and it looks like it’s maybe 1/64” out of flat. Are there aftermarket manifolds available? Or does it make sense to get a machine shop to make me an aluminum one? Can I grind out the crack and fill with epoxy?

Someone on the site will have a good spare i'm sure. With the carb if ya running an Oring in the groove in the carb flange don't run one fatter than can be squashed in the groove or it'll pull the ears around on the flange.