For the amount of time and effort to upgrade to the "stock" 9 speaker system, it will be far easier and cost effective to go aftermarket.
On my old patriot 2008 I had the stock 4 speaker system. I put in a sub box in the rear where the factory Boston acoustics sub went.
Check out this post
Custom sub box for sale - Jeep Patriot Forums
I then replaced the factory cd player with an aftermarket one, along with all 4 speakers.
Compared to the Boston acoustics system I have in my compass now, that did sound better, and if I was to do it again I would have went with the factory system, and not gone with the boston acoustics system.
It's not that it's a bad system but a simple aftermarket upgrade makes it sound better. I found the bass on the BA system quite lacking and added another subwoofer to it, but just in the back cargo area.
As for upgrading to the BA system you will have to take your dash pad off to access the tweeters that go in the front as well as run wires. For the rear hatch speakers (the ones that fold down) you'll need to get those as well.
Prices on the factory audio components are very expensive, it really isn't worth it to go that route.
I haven't replaced a factory cd player with another factory cd player of a different model so I can't help you there.