Find a stock airbox or fit different carbs, The $200.00 (US) Dynojet carb kit may work (never tried one) but without some serious modification to carb bodies it will never run right. It isn't that tey are CV carbs but the specific type of CV carb.Even Honda knew tey screwed up when the couldn't get factory race bikes to run properly with 'stock' carbs for Superbike series in the 1980's. As your in Oz you may find someone who understands CX500 carbsand knows how to mod them. mods won't be the same but will be similar.
Oh, is rear tyre fitted properly now?
The cheap pods are more trouble than they are worth (you have the cheap pods, looking at pics)
K&N 'oval will be a lot better, those actually restrict airflow at high rpm
Usual reason for bad charging is bad earths (ground connections) You'll ave to fit extra leads from crankcase to frame and probably from frame to forks to make sure headlight gets full voltage (even with all te ground leads Honda fitted)