Have a 1999 yamaha 1200 xl limited waverunner only clicks at the starter relay when trying to start it after a friend forgot to put the plugs in and it got water in the engine compatment

You need to start at the simple stuff. Check the spark plugs and see if they are wet with gas. If not, could be a fuel pump issue. See if the plugs are fouled, change them and check for spark. If you have both, it should at least sputter. Check for water in the fuel.

The start stays engaged the entire time? I would guess it's a bad ignition switch -- it would be sending power to the starter (through the solenoid) regardless of if you switched it off.

Maybe it could be a bad starter, too. I'd start with the switch.

See page 46 of the attached PDF manual (page 2-19) What you are actually seeing is "EXHST" which indicates the exhaust temp is too high. http://www.yamaha-motor.com/assets/service/manuals/2001/lit-18626-04-01_360.pdf

you may have an air leek on carbs or its running too lean

nissan altima wiring diagram Google Search

if its xlt 1200 its inside the big black electric box at rear of engine ! unbolt it and remove the back cover !

itmay be a dyna start

Follow the wire back from the starter. It should bring you to the relay. Many starter relays have 3 wire going to them. Usually, 1 smaller wire, and 2 larger wires. One wire will be power from the battery. The smaller wire will have power when the key is turned to start. The third wire will carry the battery voltage to the starter during starting. good luck

Starter solenoid

Try jumping the waverunner using a set of jumper cables and your vehicle, this will rule out if the battery is bad. If you still have the same issue, check the connections. The connection at the starter or another place may have corroded a bit. Yet another option is to remove your spark plugs to make sure that your motor has not hydraulically locked. Once you have removed the plugs try and turn over the engine. You may need to ground out your plug wires if you have an electronic ignition to protect it. I hope this helps.