Oh good lord....take your time man. Manual - tranny or windows - NO!
You're going to spend $30k+ and get a base w/ roll down windows a manual trans and shytty gears
Listen, buy one w/ the bells and whistles you want, you're likely to have it for a while...and the resale price on these stays strong, so why get things that only cheapen it?
Personally, we were totally happy once we traded the '08 Sahara for the '14 Rubi...and later, I could've gotten a built 2007-2010 for cheaper than I got my '14, but I like the interior and 3.6 enough that I paid for it. No regrets.
If you're not getting a loaded 2012+ you can easily find an older one under $30k w/ all the wants you might have.
B