I believe that you are replacing the original windows and the 2 things you mention are;
1. a sticky gasket to hold the plexiglass/ glass in place and
2. A rubber seal to keep water out.
You can order both from:
South Shore Yachts Inc.
Also see my thread about replacing my windows titled, "Yet another window issue... but different."
My only regret was not replacing all of the fixed ports last winter with opening ports.