I'm currently experiencing a ~300 RPM difference at WOT (twin 496 HOs). Port side will be at 5100 RPM (rev limiter) but the starboard side will only be at 4800. At cruising (3500 RPM), they are identical. Originally thought it was props so i tried different set, but similar results. I broke port side prop shaft earlier this season, replaced it, no other damage found. Could something in the out drive cause this? Only other thing i can think of, is that the starboard side is experiencing high water pressure (i suspect it being a partially clogged heat exchanger - getting the 2 beep alarm - plan on flushing out) but the temp is within 10-15 degrees of the port side. Would high water pressure cause the motor to go in partial limp mode at WOT? I plan on sending a set of props out to BBLADES this winter to get worked on, but find it hard to believe that i have 2 sets of props that don't match. Any thoughts?

Check to see if the timing is the same on both motors.

If you are getting an alarm, you need to have it scanned.

When I had this exact condition, it turned out to be a bad Crankshaft Position Sensor on the motor that was lagging.
BUT, again, you need to have it scanned to look for stored codes. Or better yet, buy a Rinda/similar scanner yourself.
Throttle cables do stretch over time. You could simply have mismatched throttle bodies, and one isn't opening as far as the other. This is something you can test with the Rinda/similar by looking at Throttle Position Sensor values and comparing each motor.

I agree and will scan. I just found it coincidental that after i broke the shaft and replaced only one prop (because i lost the prop when i blew the shaft), I started having this issue.

This is quite possible as well. You can always switch the props and see if the same thing happens. There is no issue with running a bravo drive in either direction. Just be aware that handing may be affected; but you should be able to do a quick run up the RPMs to see the what happens. Obviously docking would be a bear to master. Best thing to do would be to pick a beach or whatever to nose up onto, switch the props, and then come back in after a few minutes to switch back.