That boat wasn't by any chance designed with an alternate exhaust route was it (stationary outlet vs, cruise speed)?
Does that side sound different than the stbd? Does the engine exhibit back-pressure issues ( if not , the problem wouldn't be in muffler , flapper or exhaust hose, but would likely have to still be in the RW only passages.)
If you disconnect the RW hose at the riser inlet and put the hose in a 5 gal bucket, can you fill the bucket in 15 seconds at 4000 rpm (engine cold, gear in N)? What flow at idle?
Do FWC Mercs have the spring-loaded RW flow control balls? (I'd imagine no, ...but maybe?)
Do you have RW system lubed/cooled dripless shaft seals as an alternate route for water at low flow??
On the suction side of the RW pump are all hose clamps tight and strainer seal intact to prevent air intrusion until moving boat scoops water to allow proper RW pump priming?