Hi, to second what mark said. we found silicon eater did a good job at cleaning the surface and followed by a careful sand. Personally I would recommend replacing windows like for like.. I believe a boat with mismatched or non-original windows would effect the sale of the boat (but thats just me).. We refitted the frames used arbomast BR which is a brilliant product (better than silkaflex) as it doesn't cure.. our windows leaked like a sieve before we removed and refitted with this.. (Use black silkaflex to reinstall the glass to the frames if you are doing that)
A good friend of ours, Jean-pierre restores windows although he's in maidstone (Hadlow Marine) (I notice you are showing as rainham essex).. if you have the windows I'm sure he can help..he can supply everything marine window including the rubber www.hadlowmarine.co.uk.
Good luck.