First off, only change one thing at a time, then test. Throwing everything and the kitchen sink at something before testing can often bring up other issues that you'll then need to pin down.
I'd remove the skeg protector first, then run it and see how it does.
From research I've done the consensus says a prop shaft height of 3.5-4" is usually most desirable provided your setup will maintain water pressure.
Just because it's blowing out doesn't necessarily mean it's too high, it might just be too high for that particular prop. Modifying that prop or running a different prop all together might be what's needed to get the best performance. I'm running 4" shaft height right now so my anti-cavitation plate is well above the bottom of my hull (1860 mod-v), and while I do need to have some prop work done to make it even better, my rig runs better than it ever has this way and maintains water pressure.
But I agree with the above, to give any real advice some more info is needed.