As for lighting you could get a whole new top and change it to MH or you could see if you could get a higher wattage PC. The stock BioCube come with a 10,000k and a actinic (Blue) light, but you could upgrade to a higher wattage actinic and change the other bulb to a high wattage 50/50 bulb and that should let you keep a lot more stuff but am not sure if you would be able to keep clams and SPS but they might do ok if you put them up high
As for the filter this is what i have done to my 14g. I took out the cartridge in the first chamber and put the heater and 2 foam pads to keep out big stuff, then in the 2nd chamber i took out the bioballs and put in a bag of denitrate (only because i had a nitrate problem) but you could put in a bag of amo chips, carbon, ect., some people put lr rubble in that chamber to help with biological filtration. In the third chamber i have a bag of carbon where the other sponge used to be (since i took the cartridge out that had carbon in it). On top of the drip tray i put filter floss, and cut the overflow to the driptray to increase flow. You could also put a larger powerhead in place of the original or just put in an extra one in the tank to increase flow for corals.
Hope that helps
, also look around at other threads and people that have a biocube 8,14, or 29 and see what they have to say