OK, my port engine had a ticking noise, Sounded like lifters or some valvetrain noise. Well my mechanic said run it for a few hours and see if it goes away. (this boat sat all last year). Well after a couple hours of running it did go away, but I can only get 4500 rpm out of that motor and my other motor is at 5000 rpm. Any ideas on whats going on? My cams idle pretty rough, so I cant even tell by listening if it is missing or not.

Is the timing the same on both motors? I have 2 ignition modules on my boat just in case 1 goes out and just for the hell of it I tried the other 1 and I lost 300 rpms. I couldn't understand why until I notice 1 advanced at 22 degrees and the other advance 20 degrees. The 1 that advanced at 22 gave me 5000 rpm at WOT the other just gave me 4700 rpm. I would of never guess that 2 degrees there would be so much difference.

check the tach's.

DID YOU TUNE THE MOTOR UP BEFORE YOU RAN IT?
PULL A FEW PLUGS AND SEE IF THEY ARE WET IF YOU FOGGED THE MOTOR WHEN YOU PUT IT AWAY THE PLUGS
ARE NO GOOD.

OK Engine sounds like it is missing and tick is still there but faint. Is the lifter collapsed? Would it be louder if it was collapsed or could it quiet down a little bit. Dont want to order lifters if I dont need them?

Check compression. If you have problems with a lifter to the extent that you lose performance it will most likely affect compression. As a side note, the valve train does rattle quite a lot on these engines. Also when tou start up it may take a while for the oil to make its way up to the rockerarms. If the compression checks out you may want to look elsewhere.

Could be a lot of things causing it. Start with basics. Plugs, cap, rotor, and check timing.

Ticking could be a lifter, or anything else in the valve train. Could have a cam lobe going flat, bent pushrod, bad valve spring. I wouldn't start buying parts till you find out whats wrong.