I haven't installed a non-OEM head unit in a pre-facelift JK but I am guessing you just need Aerpro APP018 Chrysler to ISO and APP8SP4 Sony AV to ISO cables from your nearest automotive store to make it as plug-and-play as possible.
I don't think it does but I can't remember clearly if the JK uses some proprietary antenna connector.
The Sony mic is pretty good and has a nice mount with a swivel attachment but if you have Uconnect/bluetooth, you can reuse the OEM microphone through a mic adaptor cable, bypassing the Uconnect module.
I am guessing the JK amps and speakers have preset built-in crossovers and high/low pass filters, so I suggest switching off the high pass filter and setting the low pass filter as high as possible (you can't switch it off) but I might be wrong here.
The USB port has more than enough power to fast charge my phone and run two 32gb memory sticks with music that I connected up through a USB hub in the centre console, connected to my AX200 through an extension cable bought from Jaycar.
That reminds me - get a simple toggle switch from Jaycar and connect one end to the handbrake wire on the head unit cabling and the other to a ground point somewhere behind the dashboard. Run the wires for this switch long enough to reach into the glovebox. When it comes time to setup Android Auto or Carplay you need to be stationary and "engage the parking brake", which is where the switch comes in handy.
The average human walks 1,500km per year and drinks 83L of beer which means we're getting 18km/L.