I had not thought of how I am going to power the other devices (specifically the Xbee) but the plan I believe was to use the battery to power the arduino, and then the arduino to power the Xbee.
Two D cells would certainly give you enough power for several hours of operation. But connecting the XBee directly to the batteries will probably not give you stable operation. The specs for the XBee modules I looked at said they take from 2.8 Volts to 3.4 Volts. I'd put a low dropout voltage regulator in there to stabilize the power. Something like: ww1.microchip.com/downloads/en/DeviceDoc/21826b.pdfUPDATE: I did the math wrong. If you wanted to use that Microchip voltage regulator, you would need three D cells.
Only 1 hour - that should a snap.Given where you are currently at, I would still try the ~16 ohm series-R in the power line from the 12V battery, as the easiest fix. OTOH, in pretty much all of my creations, I use rechargeable NiMH AA cells. [forget non-rechargeable]. This includes most of my robots. Current NiMH AA cells have energy store in the 2200-2500 mA-hr range, and should run even an XBee-Pro for about 20-hours at 50% transmission duty-cycle. Also, of course, you can choose the #of cells to wire in series to fit the application. I use 5 or 6 cells in my robots that use R/C servos. The same should be good for powering your Arduino board, and the v.reg shouldn't overheat. 6 cells might bebetter than 5 cells, as individual cell voltage drops to about 1 volt when the energy is depleted, and 6*1V = 6V,which is about the low end to keep the v.reg from dropping out.
The Rev of the Uno will determine how much 3.3V current is available. The later revisions had a seperate 3.3V regulator which I'm pretty sure are more capable than the 50mA that the FT232 was capable of supplying. Have to check the schematic for your board and see what is used.
Can I use the 3.3v pin slot on the Uno to power the Xbee?
Or maybe a board with regulator built into it:http://www.sparkfun.com/products/9132
Not enough to handle an XBee Pro when transmitting.