Second for
@Leojay (and others) tips & pointers on the causes and solutions - very easy diagnostic and fix that may save you from hell and headache later
... ours just so happened to be rear bearing grease just needed love and attention: “smooth as butter” now. Very easy to pull the pump and run the engine... that will tell you right away if the rattle is the intermediate bearing inside, or at the impeller - housing/ring (high-spot issue mentioned) or with rear inner/outer bearings. When you pull the cones, inspect for water intrusion.... which could point to the problem and needs for more comprehensive repair work to the bearings).
Get supply of the gasket maker, thread lock for the bolts, and Yamaha Molybdenum grease (for use on the spline into the intermediate shaft), and a grease gun with marine/waterproof grease with injecting needle to get that fresh grease in as far into the outer/rear bearing and push out the old grease. (As best as possible step short of more involved pulling apart the shaft and bearings....). Freshen up the O-ring seal. While pumps off and your there, you may want to re-caulk the jetpump tunnel, grate joint/seam, etc. for smooth intake water flow, and tighten and seal the impeller shaft through-hull as
@Leojay points out also (that leaks sometimes)
Photo of crappy rear bearing grease, and injecting new marine grease:
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