#1 depending on what kind of area you are leaving you jeep in, i would seriously consider taking everything of value out of your jeep and leaving the doors unlocked. I saw this advice a while back on this site and didn't take it. I locked my door and now I have a giant cut in the drivers window. If someone wants in your jeep bad enough to pull on the handle and see if its unlocked, they are gonna get in it. Once you have a hard top its a different story.
As far as a lockbox idea... I think its great. I did what your are thinking about doing. I looked at lock boxes of all different shapes, sizes, and price ranges. I ended up buying a truck bed toolbox from ebay. It cost me about 100 bucks in all. It was a little over 30 inches wide, 22 inches deep, and about 15 inches tall. If you are interested in seeing pictures of it you can email me @ email@example.com
It fits PERFECT in the back end (with no seats of course) and I really like it. Its exactly what I need to keep my fire and EMS gear locked up. It actually fits so snug that Im not sure its ever coming out.
#2 As far as the stealing of the jeep itself.. Well I kind of went the expensive route and just got the removable steering wheel from Grant. I love it. Its easy to take off and put back on, and I think it will really make a thief think twice when they walk up to a car that doesnt have a steering wheel.
The reason I am happy with my "No Wheel, No Steal" method is just because no thief is gonna break into a car that they cant drive away. For the price it was worth it to me.
The first thing I bought when I got my jeep was tuffy locks for everything. Im happy I did... Still never had anything stolen, just one damn window cut.
#3 I think the decoy key is a bad idea. I think a thief knows what to look for and a key sitting out is definitely one of them. I dont want anyone breaking into my jeep because they saw a key that they thought would start it up.
#4 I dont know whats going on in this question... Why doesnt your jeep have locks? I dont think your idea sounds like a bad one tho.