^Parts 12-14 all come together as one part number (stupidest thing ever). Once you get the tranny and shifter in, you wouldn't have to modify anything as far as the console is concerned. Just pop out the automatic tray and pop in the manual trim/boot combo.
Certainly possible. The 5 speed manual (MA5) could be ordered with the full size console (D06) in 2004-2006. Starting in 2007 this combo wasn't available in crew cabs.
You'll need the steering column surround pieces from a 5sp, the shifter and boot, and trim ring from the 5 speed. You also need the pedal assembly from the speed for the clutch pedal and of course the manual transmission and components.