The lack of air supply to an engine is quite common and a result of bad practice. Having been in the engine business, we conducted commissioning tests which included measuring the air supply to the engine. Often we had to insist that extra holes were cut or a blower installed.
On Fyne Spirit, the engine was purchased two years before the boat was launched. It certainly supports the appearance that the boat was built around the engine. No pathway for air, and appaling service access. I am hopeing to pur the service access right in Malaysia by rebuilding the engine box completely. The other problem that comes for restricted air supply is the black stain that appears on the hull/transom in the area of the exhaust outlet. After any extended use of the engine we would have a sooty coating over the back of the boat. My first attempt, cutting in an engine room vent reduced the soot, but it was only the installation of a blower that fixed it completely. The soot of course comes from incomplete combustion due to lack of oxygen.
1/2 inch between coupling and seal seems quite close if you have flexible mounts, and the thrust is taken on the gearbox.
To Sailmon, 30 hp seems a bit on the low side for a 38 footer, but there are a couple of things to look at before going to repower.
Propeller efficiency is one. The bigger and slower a propeller is, the more efficient it will be. I had a 35 footer with a 30 hp engine. I changed the gear ratio to 3:1 and went to a larger prop and got consierable improved up wind motoring. There was of course a drag penalty when sailing. Prop size and speed is always a compromise.
I once had a thirty footer with a similar performance, very good in light airs, trotted along nicely, but could barely make any headway in strong winds. It had a severely over pitched propeller. When I set the propeller up correctly, it not only fixed the upwind problem, it substantially reduced fule consumption. Previously the engine was nearly always in a state of overload. Not good.
When over propped, the overload situation prevents the engine reaching full rpm which means it cannot develop its rated power. An over pitched prop can turn a 30hp rated engine into one that can only develop 15 hp, plenty for light airs, useless when real power is required. By carefully setting up engine,ratio and prop size to give maximum thrust, which will be bigger prop, bigger reduction, pitched to allow the engine to reach full rated rpm, the performance of a 30 hp engine can easily be as good as a 40 hp with a small fast prop. But there will be more drag from a sailing point of view.