Re: what to use to glue alum to gelcoat?
Well, first, I'd suggest following the manufacturer's directions... if you pre-drill/fill the screw holes correctly you won't get rot problems. You'll probably have less overall problems too if the lights require a cutout hole.
If they're surface mount, just glue them in place with 3M 5200. If you have a clean surface to start with, not only will they never come off but you can seal behind them too.
If they require a cutout, then follow the install directions... you don't want a hole in your transom plugged by a glued-in light.
Erik