I was finally able to figure how to connect a source directly to the DSP!!!
After trying multiple cables, plugs, DACs and settings, I have it working! Now I can completely by-pass the factory head unit and very conveniently connect anything to the DSP as a source. That way I don't have to deal with any of the issues of the factory HU... Though it hasn't been giving me much grief, I still wanted to have this second connecting option and also have the ability to play FLAC files directly to the DSP.
The one issue I will be having shortly, is that the Wrangler's audio is set-up to were it cuts output when you remove the hardtop, and it's quite noticeable from what I am reading on the forums... Apparently, this is so you don't try to compensate for the top being off by turning the system up even louder and blowing your speakers.
With the DSPs remote I can save 4 different tunes and switch between them on the fly, so now it's easy breezy!
What made this whole thing a little tricky for me is that the MiniDSP requires a digital source via optical or spdif and I only had analog sources (phone, laptop, tablet, DAP, Mp3 player, etc.). So I had to get a little DAC that would convert my analog sources to digital and connect via spdif or optical to the DSP. DONE!
My initial thoughts are that it sounds good with a couple of FLAC songs that I played just from my phone, but most notable is the increased output... I'll spend some time on tuning once I get a nice little DAC that will be the optional music source.