Can you just move the cmc up on the transom by using the other bolt holes that are already there? Mine has several holes for different heights and the bottom has a slot for adjustment. Worst case scenario just drill new holes. It ain't that big of a deal.
The bottom holes you could silicone and puts bolts back through. The top holes you could either silicone a thin piece of metal over them and then sandwich it on with the CMC or you could put a bunch of silicone on the CMC and hope it sits flat enough that it seals them off. I would silicone a thin piece of metal over them and sandwich it on.What about the holes in the boat? Just put bolts in them.
It may cost a little to do this, but it is cleaner than patching holes and will allow you to use the existing holes you've already drilled into your transom. Take your CMC to an aluminum fabricator and have him weld you a 2 to 3-inch extension to the bottom of the CMC. You can then raise it up to the height you need on the transom and use the existing holes. I had to do this to mine when my dealer installed it incorrectly and it has worked just fine. Cost me roughly $75 to get the welding done.What about the holes in the boat? Just put bolts in them.