I would check the ground.

So I put it to a better ground...and now all the music, not just the sub, is choppy like a poor signal. 

then you didn't find a good ground. pull your main fuse and check everything and make a better ground. 

I've tried a few different grounds, cleaned and prepped the metal, they looked solid. 

I think the intermittent sound is a different issue now.  It's with all music (Bluetooth, tuner, etc) and all speakers, so possibly a connection at the headunit?  The headunit and stock speakers were working fine yesterday even with the subwoofer issue, so I probably messed something up.   I'm pretty bad at this stuff. 

You need to stop and get help from someone who knows what they are doing before you ruin your equipment.