Get two RE8's from the group buy and the set of comps. Maybe put some coaxials in the soundbar. And then get a five channel amp capable of 1 ohm on the mono channel.
I would get a 10 inch and build a custom box. That is what I did.
As far as theft goes I through in a viper alarm with motion sensors and mecury switch in the rear. When the top is down I sometimes forget and toss my backpack into the rear seats and before they even hit the seat the alarm goes off. Good stuff.
I am putting a sys in my wrangler now too. What I have done is a Clarion 845mc HU, Infinity reference plate in the dash and 5.25 in the soundbar these are run off a clarion apa450 amp and yes you can hear them with the top down. For the rear fill I have 2 punch 8s that I am running off a Kenwood 7201 amp. I have the 8s mounted in a temp box so I can try out different placements to see what sounds the best.