I think you just need a little bit more experience with your boat in differering sea states (no offence meant - just my tuppence worth). I have a wee 4 metre boat with a 40 hp on the back - flat out speed is 31 knots on gps (flat calm, solo, fully trimmed out), so our rigs are similar. Any wave action reduces that performance considerably - not that the boat isn't capable - its a matter of comfort and safety. In the type of swell you mention (3ft) I am probably doing just over 20 knots, but backing off just before cresting the wave, then power on again to drive down and up the next one. It ends up being a very smooth rolling action - and keeps airtime and slamming to a minimum. I nornally keep the motor trimmed in in anything other than a flat calm - in my wee boat it doesnt make that much difference except in flat calms. The boat behaves well like this, and my ears are saved the verbal abuse from the missus sitting on the pillion! The frequency of the swell (space between waves) is also critical, as closer, steeper waves are not as easy as longer, spaced out ones. Having said all this, I don't get it right all the time, and sometimes get caught out by a wave, and find myself airborne big time, complete with big slam back down. It isn't comfortable, sometimes the boat gets a bit skew-whiff too - the solution is in your throttle hand - ease off a bit! Like I said at the top - I think you just need to get more used to handling your own rig in different conditions. I have also tried doel fins on my outboard, but found the boat behaved better without them, so took them back off.
Of course every now and then I get to pretend I'm young again, and I'll blat round flat out jumping every wave in sight. You still need to exercise throttle control just before takeoff, or the boat lands every which way. This generally doesn't last too long 'cos its tiring and I eventually scare myself too much on a bad landing, so the red mist clears and I back off a bit again. Just enjoy what you have, and as you get more in tune with your own rig you will find your own limits and be confident within them.
"Remember the Plug!"