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What kernel are you using? What are your CPU settings?
If your kernel is set too high or low, it can cause that to happen.
I don't know and I don't know. How do I check/change them?
Use kernel tuner and check the cpu settings, let us know what your values are.
Well your settings are fine, I would do a wipe and reinstall the rom and see what happens. You can save battery life by lowering your min to 384 and not have any lag.
I must not have flashed it over properly the first time. Indeed, the ROM was running and NOVA was active, but the background and particular settings remained stock. I just performed a full wipe and loaded Midnight. It seems to be running much more quickly now, and there are even less unnecessary wares on the phone. Hopefully this fixes the problem.