4500 sounds even quite low for a 50 horse, depending on the model year.
It sounds like you have a couple of issues.
First off, you have been running "too much prop". A pontoon boat is very difficult for an outboard to push - it just doesn't want to move through the water very well. That is, in part, what led to the development of "big foot" motors which have lower gears and turn somewhat less pitch props than you would find on the average boat.
So if it was only making 4500 rpms at it's best times, you probably have at least 3 or 4 more inches of pitch on it than you should be running (so if you have a 13 pitch prop, a 9 would probably be more in order as an example).
Secondly, now that you have been overloading the motor it is probably significantly carbon fouled. So before even attempting to select the appropriate prop for this rig, the motor needs a de-carb and major tune-up. You have to at least get it back to it's potential before you try and get it running the way it should be...
On most 50 horse Merc's built in the last 30 years or so, running below 5000 rpms (not capable of reaching that at max, even if you run consistently slower) will severely shorten their lifespan and can result in significant internal damage...