I followed Main Sails instructions and I just completed a project where I replaced all 6 ports on my H34. (thanks for the great help, I never thought I could do that until I read a bunch of Main Sails articles)
Main Sail -- this is your page right?
Installing New Found Metals Stainless Portlights Photo Gallery by Compass Marine at pbase.com
Anyway, at first I tried to seal 2 of my new ports with polysulfide calk and I realized that I did not have enough skill to get a good caulk bead. So I switched over to using some gray butyl tape I purchased from Main Sail. It worked very well as did the ball/ stab n' pull method to remove all the excess material. I used a dull putty knife as a blade to score a line in the butyl before I pulled the excess away. It looks very professional now.
Insofar as your cabin liner goes, I had a similar problem. To strengthen the area between the hull and liner I used expandable spray foam from Evercoat. The foam is also water resistant so it will further to help seal that area of your cabin.
To apply it I used masking tape to seal off the inside of the port and sprayed it from the outside. Make sure you mask off the port because as the foam expands it may want to drip into the cabin and clean up is not fun. Also, make sure you support the liner and the cabin side with some sort of clamp as the foam may want to expand outward and distort your liner.
After the foam is dry I used a Dremel with a sanding bit to smooth out the opining. (once again it is a good idea to keep the inside masked off as this step produces copious amounts of dust).
With the opining all smooth and ready to go I put the new ports in.
The one trick I learned with the butyl tape is that I cut it to size and applied it one section at a time vs. trying to wrap one continuous loop around the trim ring. I.E. I would cut a pieces for the top, left, right and bottom sides, bed them down with the wax paper still attached and once satisfied I removed the wax paper and worked the butyl together to fill any gaps.
After I did that project I used some of the gray butyl tape to re-bed most of my deck hardware and a deck hatch. So far I have not had any leaks and I am sold on the material as a great beding material.
Good luck with your project!