The Tj unlimiteds aka the lj's were only produced 2004-2006 so those are your options for years. Out of those years the rubicon was only produced in 2005-2006. I believe that the 04's only came with an automatic transmission if that matters to you as well. If you don't care about the rubicon options or the automatic transmission I would go for the 04 since they don't seem to have the fearful oil pump drive assembly failures that several 05-06 owners have had, other than that possible problem and the already listed differences I believe everything else is the same.
I personally like buying vehicles stock, that way you know what's done to it and you know it's done right as you build it. Sorry can't help you on the stereo, that's about the last thing I would ever put money into.
2006 Rubicon LJ, auto, 2" lift, 1.25 bl, mml, tt, armor, winch, 33's, that's it for now.