I cut the wall using a couple of really sharp kitchen knives...which are now probably dull :P
The plastic was tough to cut but I managed to cut into it enough that all I needed to do was take a pare of pliers and twist/pull it off. It's not a 'clean' looking cut by any means but it certainly increased the water flow by a LOT! I also started taking out some more of the bio-balls. I've been taking out the bioballs little by little over the past several months, and I probably have 1/2 (or a little less then 1/2) of what the BioCube originally came with. The only new problem that I've noticed is that with the removal more of the BioBalls combined with the huge increase in water flow there's a pretty significant increase in the sound of running water in the back chambers.
It's not a huge problem, but if you have any suggestions to muffle that sound I would definitely appreciate it :)
*The protein skimmer doesn't have anything to hang on to and the suction cups are kind of useless. However it still sits wedged in that first chamber, kind of resting on the chamber floor.