In that year (1999) the 220HP would be a carb'd 5.0L.
You should still get the same exact speed out of the boat. The difference, though, is that you won't be able to use all of the power (you'll over-rev) without re-propping or changing the gear ratio. If you're losing speed, there's either something drastically wrong with the engine (not making full compression), maybe something like a dirty bottom, or there's user-error at play.
What type of motor did you put in?
EDIT:
Bill, for what it's worth, even if he originally had a V6, it wouldn't matter. The reason is that the new engine will still spin the outdrive up to the same revolutions (and, in essence, the prop) as the old engine did, which will mean the same top speed. Let's use the max RPM for the old motor as an example, 4,800RPM. The new motor will still turn 4,800RPM (which in leads to the same RPM's for the prop). But the difference here, is that the new motor will spin up to 4,800 with much less throttle input than the old motor, which will ultimately allow for the use of a taller prop. The taller prop will then allow for full throttle and increased speed.
But, along the gear ratio line of thinking, there could be an extreme case where there's just too much "new" HP that a prop, alone, won't solve the over-revving problem and a new gear ratio (and probably still a new prop) will be needed. However, even if he had this "extreme" case, he should still be able to get the same top speed out of the boat with the way things are now.