Hi elliotm,
Don't know how big the holes you made are, I made a single 2mm diameter hole in mine, and don't use cotton wool. Maybe an idea to cover some of the holes and build up until you get it how you feel is 'best'. Pain disassembling / re-assembling I know.
The crossovers you see in the cable-side can are there to account for the sealed back, so these drivers will be way too bassy and even start to flap if you open them up too much. The backs are too small to make effective baffles for the holes to try and prevent flapping, so you really do have to play with the amount of cotton wool and the number/size of the holes til you get it right, or undercut to start with and be happy that while you might improve them even more you might also overdo it.
I haven't noticed any imbalance, there again, you can see there is uneven 'porting' in the cans, for EG where the cable goes in and you have to remove the tape to get at the screws. The sealed back will not show up any difference as these will not effectively be 'ports'. The more you open up the backs though the more these will openings affect the sound of each can, so maybe you have made too big and too many holes? You could try taping over these open areas (where you removed tape to get at screws etc) until you can even them out? Or reduce how 'open' the backs are (cover some of the holes you made) until the open areas don't make any difference anyway.
That's why I started small, tested, and was so happy didn't go any further, but maybe I'm not such an adventurous modder?
Another idea might be to bypass the crossovers in the cable-side can. This should allow you to open the backs up as much as you like as, apparently, the same drivers are used in fully open back models. I don't know if they have crossovers to alter the sound characteristics in those open back models, so it's all 'play and see' I'm afraid.
All part of the fun of modding I guess.
Regards
David