Do all the above,
There is a plethera of things that can be wrong. Very little info to troubleshoot. did it always do this or did it just start? Are you getting good cooling ? Check the pipe it should not be too hot ( sizzling ) . Does it have a pisser and is water coming from it ? Sometines the starter is right next to the pipe on some models. You have to rule out some things , try to jump the starter straight. Sounds that heat is effecting the ski because after it cools it is good ? A good place to ask some questions is PWC Today. There are quite a few knowledgeable people in each forum. Most of my stuff is old school & modified stand-ups. Check out the yamaha forum and do a search. That way you don't have to get activated . A lot depends on how( what words you search for )"like yamaha 1200 gets hot & shuts down". If you can post ( sign up ) and ask for help, you will get some. Hope that helps.