My boot leaks water, I'm sick of my sub and amp getting wet, so does anyone know the most common places that 2nd gen boots tend to leak from?

most common boot leak is tail lights. but check rubbers. pull them up and look rust hole,s or stick a mate in the boot with a touch and spray boot with hose (like it raining ) while he look were the water coming in

As magnaman89 said, best bet get a willing mate to hop in the boot with a torch and look.

Is it dripping in or could you have a small rust hole in the bottom and spray is coming in and wetting stuff? Maybe pull up your carpet in the boot and have a look-see for rust or holes/grommets

Tail light seals. If you can dry it out and feel where it starts to get wet again, or pull all the carpet out and look for leaks dripping down through the seat hole hatch.

To replace the foam gasket all I did was went to Clark Rubber got some 4mm foam stuff and trace around the old one gasket. Reinstall the new gasket to the tailights :)