Hi Pasty

you could be putting a lot of stress by taping it in with a mallet. Of course you will be the best judge of that as you are doing it. I'm confident you are okay. I'd suggest you take a look with the dry fit, to make sure nothing is being cracked, or that the fiberglass has not whitened. If so you should make the gunnels slightly less tight.

How much will the epoxy add?... I think not much as it should squeeze out. however it if is really tight, it may become a dry joint.

I recall having lots of 'fun' getting my gunwhales in place, In my opinion, one of the hardest parts of the process. If you have it going in with a dry fit you are doing well. I found the epoxy acted a bit like grease. It was harder to get it to stay in place with the epoxy on, it would slide a bit.
I did not use screws, and suspect that would have solved my problems in this area.

Good luck, sounds like you are almost there.

Myrl