If'n it was mine, I'd get a new intake. Curt(a member here) does a really nice ported intake, and usually has a listing in the classifieds. He will surface the flanges and solder the AIS
port shut also, if you want him to.
Use the blue heat and fuel resistant sealer, that doesn't harden. Hylomar is one type, and Permatex makes a product called Permashield that is very similar. Apply just a little bit to the surface of the flanges, outside of the ring seals. Yamaha uses grease instead of the sealer. The grease and the sealer help the flanges to slip and slide as they are snugged down. The nonhardening part of the sealer prevents deforming the flanges. The silicone type sealers can result in a canary under the carpet scenario if you're not careful.
Theres a real good chance the manifold is leaking somehwere, simply because its the nature of the beast. They are prone to developing a leak at the head to manifold flanges, and you can have a devil of a time finding it. If you can ease the enricher out just a bit, and it runs better, then you know you have a vacuum leak somewhere.
Its not really a choke. It actually adds fuel and a little more air, when you pull it out. The bikes appreciate being rich until they warm up a bit. Having the proper tension on the enricher will help.