As I stated above. You can most definitely get a Rubicon without power do-dads (except A/C is standard). You may have a hard time finding one on the lot, but you can order it that way for sure.
Go to Jeep.com and select the build and price on a Wrangler. Power windows/locks are an option as are the half doors. Cloth seats are standard. A base 2 door Rubicon stickers for $31,990.
http://www.jeep.com/hostc/bmo/CUJ201406/models.do?
Here's one near me, with half doors.
http://www.chrysler.com/hostd/windowsticker/getWindowStickerPdf.do?vin=1C4BJWCG9EL157727
The plastic bumpers are made to be tossed and are worthless. The carpet and roll bar padding are easily removed. Many people spray Line-X or similar inside, which is the plan for mine.
Don't throw away those 32" BFG KMs before you use them on a tough trail. They are surprisingly good.
My Jeep? A base Wrangler with a set of brand new Rubicon wheels/tires bought at a give away price. It surprises the hell out of me every time I use it off road. A 4-1 low range and locked difs would be over kill for what I do. But the 4.10 gears would be nice.
Sadly, those Rubicon difs only lock in 4 low, but I hear there is a work around for it.