For your air in the top of the canister problem...
Remove the pump, install a small bulk head fitting hooked to the same diameter tubing you've been using then relocate the pump in-line. This will not only suck all the air out of the filter, but also eliminate the extra hole needed for the power cord. You could even get fancy with this set up and hook up quick connect fittings. Dr Fosnsmith sell some that would work.
Nice DIY BTW.
