Sounds like a job for 5200. 'Window seal' and silicone will NOT keep the water out for long. All silicone does is take up space-- it fills gaps and does NOT seal watertight (for example, under the waterline a silicone-sealed seam is an automatic leak). If the affected area has already been 'sealed' you won't be able to get anything else to stick. This is why for plastic ports, Lexan, Plexiglas and the like, I ignore the warning 'use only silicone caulk to install' and go right to 5200 from new. Using 5200 from new is a surefire way to avoid leaks in future. So what if it melts the plastic just a little bit-- if it's sealed right from the off it will not leak in future. And the issue of removing the window can be solved with a dulled chisel bit and a new window... because by that time the boat will be so old you'll want to change them out anyway.
For the Lewmar aluminum ports the premise is the same... if it's been done with dum-dum/butyl tape or silicone, your first task is to remove all residue reliably before anything else will stick. Or, you can go with what was used before, and have this fun all over again when this issue returns in future.
BTW the secret to removing 5200 is to do it mechanically using appropriately-sharpened scrapers, patience and brush thinner or gasoline (a little at a time!) as a solvent. I've never had a problem with this, even with removing 5200 from wood.
