I am NOT an expert on these things.... I'll leave that to TheFermanator and SpareParts. However, having just said that, it sounds to me like something is drastically wrong. A 200HP engine should be producing a lot more than 29 MPH at 5100 RPM IMHO. So I'd be looking at two things.
1) You said the lower is a replacement. What does the factory call for as a final ratio, and what is your lower producing?
2) Is your prop an original Raker or a Raker II? The Raker II's have a lot more cup in them for the same pitch and dia. and that could account for a lot of your lost RPM. So (and I know this is just a guess, nothing more) if the reworked prop was worked to Raker II specs and your original prop was an original Raker then they added more cup to the prop and that would account for your loss of RPM.
Use this link to calculate:
http://www.rbbi.com/folders/prop/propcalc.htm
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1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
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