First step is to plan and buy your Megasquirt. I used a v3.0 board and a MS2 processor. http://www.diyautotune.com
Currently, the latest board release is v3.57 and processor is MS3. However, you do not need a v3.57 board to install a MS3 processor. It will work for either board version.
I recommend a V3.0 board because it currently has the best documentation. However, the 3.57 board is pre-assembled if you are not handy with a soldering iron. If you choose a 3.57 board, you need to know this information to use this write-up.

$430 Includes MS2 processor

$253 not including processor.
Processor choice is completely up to you.
The MS2 processor has the best documentation and is easy to set up and use. However, it only has a limited number of inputs and outputs and cannot handle advanced engine operations like sequential fuel injection.

$96
The MS3 processor is very new and much more advanced. It is highly expandable and is for a true enthusiast.

$199 This article however, only covers the MS2 processor.
You can optionally buy the Megastim. The stimulator acts as a 'digital car' and is used for assembly/testing/flashing purposes. I highly recommend you buy/build one. It can be good practice if you haven't used a soldering iron in a while.

$45