Time for some updates:
I went out for a run today, and she seems to be doing better. The water was pretty rough when I went out the first time (1-3 footers, I would say), but it was a fun ride. We were out for probably an hour and a half in all. I made several speed passes in those rough conditions, and managed a top speed of 57mph. Not bad for the conditions! ... 1mph slower than my previous top speed recorded on flat water! The RPMs were also higher... the rev limiter was actually kicking in when I'd air it out, and she was running a steady 100-200rpm higher. I didn't let the boat idle much, though. If we slowed down, I staid on the throttle a touch to keep the RPMs up. When I got the boat back on the lift, I pulled the plugs. They weren't new... have 3-4 hours on them now, and the last set only lasted for an hour or so. The front plug (the one in question here) was slightly wet as opposed to dry like it was. The back plug was still slightly more wet, but that could be because I am not using new plugs. Both of the plugs were brown in color as opposed to black (like a chocolate color).
The water calmed down a bit just before dinner time, so I went out for a quick speed run. The water was still choppy, but the waves were no larger than a foot in height. I manged to obtain a top speed of 61mph at with RPMs in the upper 6700's to low 6800's. With the second GTX RFI, I manged to get 62mph with RPM's just slightly higher (upper 6800's to low 6900's).
I would guess that the one mph difference is probably due to a difference in the speedos, or maybe in the RPMs? It appears that I have fixed the probem, no? The boats are now almost dead-on equal in speed, when there was a 5mph difference before.
Thoughts? Should I be concerned with the slight difference in RPMs? Could the high performance plugs in boat number 2 account for that difference?