Randy (Goldnrod) probably gave you the best advice. You and I have a 90 HP on our boats. If you get out and try to outrun ski boats, or try to compare yours to one, then you will be disappointed. We have pontoon boats. They weren't "intended" to race around the lakes, but due to the discontent of many, they've been turned into faster boats, although, you can take your same 90 HP motor and put it on a good sized joh boat, and it will outrun some of those ski boats. I say that because the boat you have was made to cruise around, drinking girly drinks with your friends and family.
These other guys that have their pontoons doing 40 - 45 are going great with what they have, but they did spend the bigger bucks getting that 45 MPH. Again, you could take that same motor they have and put it on a low profile fiberglass bass boat, and it would be doing 70+, so it's still got everything to do with what you put the motor on.
Back to Randy's magic statement: Enjoy what you have, and if you need more speed, then pull out the wallet and start throwing money at a larger motor, under-skirting, lifting strakes, etc., then you still might not get exactly what you want. JMHO.