Mine was like that too
We discovered ours had the same clearance issue yours has. Like Ed says, you should check the alignment and fix it. You will find a very noticable improvement in sounds transmitted through the boat.
Check the alignment by disconnecting the coupling and unscrewing the packing nut and see where the shaft actually wants to point as it goes through the cutlass bearing and into the stern tube. Mine was way off and took effort to pull it to center. Support the shaft inside the boat in the center of the stern tube with a block of wood with a V cut into it. Can you rotate the shaft very easily with no binding at the cutlass bearing? Does the cutlass bearing want to direct the shaft off at an angle? ( If the cutlass is already worn out, you may have to replace it first to perform this test.) Search the archives for how to change the culass bearing without removing the shaft. If it passes nicely through the center, then realign the engine motor mounts to match up the flange faces. If it binds, check the passage of the shaft through the cutlass bearing while it is supported in the center of the stern tube. You will probably find at that point the cutlass rubber is being pinched on opposite sides of the bearing. The strut will need to be realigned (like mine did). I took it off and with the help of a belt sander, changed the angle of the flat part slightly. I mixed up a batch of epoxy/microbaloons and put it in the well where the strut goes. Put a couple of layers of Saran wrap on the strut. You do not want to glue the strut to the boat at this point. Put the strut in place with the shaft held in the center of the stern tube and in my case, support it with a step ladder and a bottle jack. That way you can fine tune the alignment. It is not bolted as the original holes now filled with epoxy are no longer aligned with the strut base. Make sure the shaft is passing through the cutlass bearing perfectly centered (not tipped up or down and straight left and right. Let the epoy cure. Trim off the exra epoxy that squishes out. You can then redrill the holes using the strut as a template. I only bedded the holes themselves with 4200 as I still didn't want to really glue the strut to the hull. After aligning the engine it has been really good ever since.
It looks like you have a good place to work on the boat. I had to do mine in the yard and pay for the storage days. There is never enough time to really spend a lot of time to do these projects right. I always have to rush and usually leave something out, which is frustrating.
Good luck
Allan