Clean/tighten the engine ground lug as well.

I have had good luck with Rainier tires in the higher load ranges.  I also like Goodyear Endurance.

I received receipts from the previous owner and it lists a Mastercraft PN filter (155199) and gasket (155102) being changed year the previous two years they owned it.  I'm starting my third summer without changing it.  The Malibu owner's manual says it should be changed each year.  It is currently running fine, but I thought it would be a good idea to change it.

I found an Indmar Exploded View image for the 5.7L's showing the fuel line routed on the port side by the transmission with the Indmar PN 56003 fuel filter.  My fuel line is on the starboard side and goes up under the plenum with no sign of a filter that I can see.

Is it the same beep when you turn the key on but don't start the boat, or a different beep?

If it's the same beep as when you key on but don't start, try disconnecting the wire from the oil pressure switch and see if it goes away.  If it does, replace that.  They're cheap, easy to replace, and go bad.

Some good advice here.  I put the trailer into the lake up to the point where just a few inches of the forward most bunks are visible above the water.  My wife puts the boat on the trailer and I basically have her idle forward with the boat in and out of gear to keep the speed low, until just before the bow crosses between the guides when she goes to neutral.  The bow catches on the forward bunks a few feet from the roller.  I click on the strap from the winch and start to crank forward.  I have her put the boat in gear with the wheel straight as I crank the boat up to the bow stop.  We sometimes add a bit more power, to move the boat forward easily...a max of, say, 1500 RPM or so.  I don't call this power loading.  If you are really hammering the throttle, your trailer is too shallow and you are going to tear up the bunks (or worse)

The KEY to keeping everything coming out of the water nicely is to go SLLLLLLLLLLOOOOOOOOW when pulling out of the water.  I can see the boat slowly move from side to side as it "hunts" for center, and when I go very slowly it works well.  If I see it not center, I stop, roll back slowly to float the stern, and try again.  

My only issue is that usually the winch strap will stretch a bit as the boat tries to go backwards when I exit the water...even going very slowly.  Once everyone is out of the boat and things are secure, I'll move forward about 5 MPH in the Jeep and hit the brakes hard while the trailer bunks are still wet and the boat will usually slide forward that 1".  Then I tighten the winch strap a few clicks and I am on my way.