Step 1: Parts, Tools, and Component Preparation
Arduino Pro Mini 3.3v (8MHz for low power use) - Sparkfun
Nokia 5110 LCD - Adafruit or SparkFun
LiPoly battery and USB charger kit - Sparkfun
ChronoDot RTC - Adafruit
Perma-Proto mint tin board and matching tin - Adafruit
Solid core hookup wire. - Radio Shack
Standoffs and screws (to mount the board in the tin. I used a kit for PC motherboards)
4 pin female header (for the ChronoDot) and 8 pin female header (for the LCD - I cut two pins off a 6 pin) - Adafruit
Two micro switches (one for system power, one for LCD power) - Radio Shack
Solder and soldering iron - For this, having a digital station helped a lot. - Radio Shack
Multimeter - Radio Shack
Dremel rotary tool or other cutting tool. I used a Dremel 4000
Panavise Junior, Helping Hands, or other tool to help soldering. - Radio Shack
FTDI Friend or FTDI Cable (to program the Arduino) - Adafruit
Build everything on a prototyping board before you even touch the the Perma-Proto board. Worry about the power switches later.
First, assemble the ChronoDot, Arduino Pro Mini, and LiPoly charger according to their own instructions. Use the headers on the top of the LCD (the ones labeled 1-8, not the ones with the text labels) and use a right-angle pin line on the Arduino programming headers so they don't stick up. There is no need to attach headers to the ChronoDot's BAT/32K/SQW/RST pins.
Attach the LiPoly charger board's SYS OUT + pin to the proto boards voltage line and - to the ground line. Connect the Arduino's VCC and GND lines to the positive/negative rails on the proto board.