The mfr is always fiddling with things to make 'em run better or last longer (at least we hope that longevity is one of their goals!). So, the baffle was an upgrade to, I'd imagine, the exhaust tuning. The fact that they superceded the old part number instead of making it a new part number, only applicable to the newer engines, kinda tells me that whatever improvement that extra baffle piece gave, would have the same effect on an older engine as well. So, maybe yours will run even better than before!
The oblong hole in #1 cylinder on the newer cover corresponded with similar shape on the machined end of the cylinder casting, and was drilled/tapped to accept an optional temperature sensor. No real advantage to that, though, as a water pressure gage is a better indicator of cooling system condition. If you were to lose the water pump, by the time the sensor registered the overheat the engine would be fried. A pressure gage would respond immediately and at least give you a sporting chance to shut 'er down before burnout.
My buddy got his Frankenmerc 50hp Shortie running today, and other than a funny little noise at the top of the engine, it runs really well. He's going to pull the end cap and make sure nothing's messed-up. The crank has a bit more than .012" end-play after replacing the crank bearings, so I think he's gonna pull the upper shim to get it back into specs.
G'luck with your project, let us know how it runs!........ed
