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...and now when the controller is on full tilt, my headlights dim...
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You most likely don't have a voltage converter as they would provide stable 12v output down to 30v pack voltage.
If You have your lights connected to just a few batteries, You are better off investing on a good (20+amps) 48v->12v voltage converter.
It is too late to reverse any damage done to your old batteries, but this will prolong the life of your new batteries when you replace them.
You should also have a digital voltmeter wired to the dash so You can monitor how low the batteries get under load.
Check the site sponsors like cartsunlimited.net for both items.