I am using pin 3 as my scope ground. Thinking about running a wire directly to the negative post on the battery and measuring any delta’s and noise between the grounds.
You mean pin 3 on the 26 way connector on the Phatbox??? That is an audio ground - depending on the box it may not be directly coupled to the signal ground for the control signals - that is pins 4 and 16 which are also the power ground.
You will see slight negative excursions on signals due to ground jumps as the Phatbox and hard disk power up, but nothing in the volts range - maybe 100 milli-volts or so.
Be very careful where you ground the scope - and I would be inclined to avoid adding extra ground wires. Get it wrong and things may go bang. As an alternative you could ground the scope to the chassis (battery negative) and then look at everying relative to that.
CD changer protocols vary a lot. I assume you have already searched for any info related to the protocol used by your head unit on the web? Another option if you just want to control the Phatbox and not worry about compatibility would be to load up an alternative firmware into the Phatbox. I don't have details, but I have read that the TrafficPro format is relatively straightforward, and there is Phatbox firmware for it.
Good luck !