Boy, that's a tough one. I am driving the Rene that you have your eye on (sans color - mines Granite). I roll around in the Latitude, manual, with MySky and the Cold weather group. It's great - I love it, especially in the cold Chicago winters, and I love the MySky in the summer. But, a dealer near me had the exact model I wanted at a pretty darn good price. Have you used jeep.com to build your and look for one locally? You can put in all of your criteria - in fact, I believe you can build a 2017 manual with the cold weather package AND the remote start. Given where you are in the country, there could be one 100 or so miles away ..... just an idea.
If that doesn't work, I guess you'll have to decide how bad you want a manual. It is a hoot to drive, but probably hurts your resale, and doesn't save on gas mileage, given the recommendation for 91 octane. There have been a couple of posts about premature clutch burnout, but I don't think it's really an issue. Most folks with the manual seem really pleased.
My suggestion, if you haven't done so yet - go to a dealer with a manual Latitude (doesn't matter if its not the one you want) and drive the manual and Automatic for a while, and see what you like. See if you really, really like the manual and want to intensify your search. Good luck!
2016 Latitude, 4x4, 1.4L 6spd manual, Crystal Granite