I'm also 5'9" and took a chance on the 20": fit is perfect, especially since I'm used to riding a 56cm 700c road bike, and the MTB I rode most of my undergraduate years is 21".
On the Jack, if the stem is too long for you, you can either get a shorter NVO stem or switch out the whole system for common 1 1/8" spacers and stem. I found it hard to fit in the trunk of my wife's Camry (go figure) but it will fit if you either (1) remove the stem/handlebars or (2) remove the front wheel (so you can turn the handlebars horizontally. The latter is the easiest option. It's a great bike overall, but be careful if you change the bottom bracket for a sealed cartridge unit: one of the screws holding the mini bike stand is threaded into the bottom bracket shell and won't screw in all the way because it will hit the sealed cartridge. The OEM bottom bracket is cup and cone. Nothing wrong with the latter however.
Lastly, Thor's a great guy to deal with. He'll take care of you and has great prices, especially on the 2006 Jack which is actually a 2007. But don't tell him I told you.
