Glad to see another 1650 ! You're going through a lot of what I've done, especially the oil pan and engine mounts. You may find OEM mounts will give better service. The 16 Hp Kohlers are real thumpers and I'm sure some engineering went into them for enough flex to not allow frame and sheet metal fatigue but yet stiff enough to hold in place for many long hours of engine time. Lots of posts and owner's stories of going home made, after market, steel, etc but OEM had the best service. New flex couplers , rag joints, with ball swivels on the driveline will also limit vibration.
I've run mine with and without the panels and they are quite a bit noisier without them. I've measured with a sound meter and there's about a 10 dB difference which is a lot especially if you spend hours mowing acres. I can say the old cub is quite a bit quieter than the neighbor's new JD, which may in part be the deck as his mower really screams or so it seems from an acre away. The engine shroud is pretty tight and channels all the air through the muffler box, I can't see or feel any relation to engine cooling with or without the side panels. If they did, the owner's manual would have cautioned on leaving them off.
Keep us posted, great to read more!