It still sounds to me like you are not getting full power. Four Winns specs for that set-up are 48 mph at 4500rpm and 50 mph at WOT with a 21" pitch prop. You decreased pitch 4" and the rpm rose 600 rpm to 4500. Unless the engine is not performing or someone has changed gear ratios in the outdrive to something noticeably lower than the 1.62:1, you should be getting much better performance from the 21p prop. The 17" should be going way over the 4800 rpm redline.

I had a similar loss of power situation on my 190 with the Volvo 5.0 EFI when I had an exhaust flapper valve come loose and created a partial blockage in the exhaust. That robbed me of a lot of power. The boat ran smooth but struggled to get on plane. RPM was 500 low and top speed was 10mph less.