I've never seen a stepped version of the P16 before! Are there many over there?
I'm no expert, but would I assume correctly thot those Stepped 16's tend to run bow down? I suspect a complete re-do of the running surface is needed to correct any handling issues you're having associated with the step, but it would be an interesting project.
It's a one off, custom job. From what I've heard the steps have never run good on that hull. They only run in about 6" and so don't make the hull a true 'stepped' designed. Personally, I would fill them in as best you can and work on upgrading the motor. If you have the money you can't go wrong with a modified OMC 70hp motor... Your Yamaha 90hp weighs approx. 80 pounds more than the similar Yamaha 70hp motor.
Steps are just not that easy to design and what might look the part maybe technically wrong. Can't say with yours though. Also more difficult to add steps to an existing design than starting with an all new design.
Also as others have said - it also has quite a bearing on set-up of the boat and how the boat is driven. So looking at centre of gravity position, engine heights and trim used, propeller type etc etc.