I suspect there is significantly more research regarding zebra mussels clogging pump intakes.
Maybe you can find a decent solution in that literature that would also be applicable to your particular situation?
I might try fabricating an easily removable intake screen, and using a two-screen solution. Swap out your clogged screen for the "clean" screen. You can then determine the easiest method to kill the colony and remove the jelly blob. If the solution involves time to dry out or time to soak in a solution of X, you now have time on your side.
Good luck,
Rod
