My biggest peeve with the biocubes is the small return pump chamber. It would shoot bubbles every other day in the summer. Drilling for a sump shouldn't be too hard, especially if you've done it before.
My recommendations would be to see if a smaller Gla-ssholes overflow would fit in one of the first two chambers, drill and install, then have the return from the sump feed directly into the biocubes return hole - completely bypassing the stock return pump. You shouldn't have to drill for the return but it might look funny looping over the edge (it wont pour back into your sump if the power is off and is less work).
Lighting is worth messing with if you got the cash for LEDs or want to remove the top alltogether (as you mentioned), otherwise you are just swapping or adding more heat and complications. I had my BC14 get to 90F two years ago in decent ambient temps. Gotta be careful.
For filtration, screw those biocube proprietary filter pads. They clog in under 24 hours and restrict flow. If you do end up getting a sump, you could buy any skimmer you wanted and easily make chambers for carbon and filter floss. If you decide against a sump, something like an aquaclear with filter floss and better branded carbon does wonders sans the bio media. Don't buy the biocube skimmer.
Truth be told, at the end of all these mods you are left with a Frankenstein fish tank that looks like a west Virginian moonshine still. This is why I bought a rimless tank and smashed my biocube with a hammer. Would have saved money if I had done that in the first place.
My two cents.