Where do I start with my Jeep?

I agree with wire brush and paint but don't forget the primer! Paint cannot get everywhere so do what you can on a regular basis. Some people like to use a garden sprinkler under the jeep to gently flush away dirt. I have heard rumors of car washes reusing water (after questionable filter), so who knows what we are getting there. I use these blackforktool.com to help keep the inside of the frame clean. Jeep left very large hardware access holes in vulnerable places. Golf balls could literally enter your frame without an exit path. And finally your best friend.........Fluid Film! It really helps! I have seen it for $100/car or $150/truck. If you do it yourself you could do the frame inside also.
 
I have those frame plugs from Blackforktool also. My JKU came from Canada also but there is hardly any rust under it. But also it's been heavily undercoated with something, it's a 2008 with 72,000 miles on it.
 
I used PB Blaster's Surface Sheild. Like Fluid Film and Wool Wax, it is lanolin based and doesn't dry. It can be sprayed on wet metal, and will pull the water away. It will stand up to power washers. Pull all skids, clean rust as well as possible, start spraying surface shield inside frame, then everywhere you can get to. Repeat every year. After a few, you'll probably be able to get away with spot spraying. It will stop the rust. Good luck!