dont use a tone, use music your hardest hitting song. You are listening to music not test tones. Test tones are only valid if you actually analyzed the recording levels of each song in your music library and you generate a test tone that matches the recording level, not some random ass 0 db test tone you find online that will literally just give you a super innacurate setting.
Power acoustik has pretty poor quality control so the actual power output of each amp can vary. Just a thought.
Since you are using a stock head unit, you are using an LOC right? raise the level adjustments on that a lot higher and lower your gains then restart the tuning process.
See if you can find a little piezo, wire that up with your sub at the same time, The impedance is so high it wont really affect the sub the buzz noise would be clipping. very fast easy method.