I have a new 540 engine getting water in the oil what would be the first things to check appreciate any help. Also new oil coolers and headers . thanks

Running in cold water without oil stat ? Oil needs to be 212 to boil it out. If not then I'd look into that chit. :-)

Before you run it again Call the builder and ask how they want to handle it !

Intake gaskets most likely This is a % bet.

Check your water psi when running also.

Other engine is fine on oil temp etc. Water psi is 20 at 5500 rpm. Also if I remove intake to reseal how long do I have to let the silicone set up before running it.?

Instantly. Which obviously will be a few hrs or more until your ready.