I'm thinking about doing the intake manifold myself so that I know it gets done properly. I will be replacing the plenum and the o-rings for the injectors while I'm at it.

Is there anything I can clean the injectors with while I have them out on the fuel rail?

Soak the ends in injector cleaner.

You don't have to change the FI o-rings BTW! You just have to lubricate them before installing them back into the holes though.