The first thing I'd suggest is print out and read the excellent documentation available for the MegaSquirt. The documentation is filled with a huge amount of information, is easy to read and follow. Parts and assembly is clearly laid out. If you can hold a pen in one hand while pointing with another, you can assemble the MegaSquirt with a soldering iron, a little attention to detail and some patience.
The first thing I did was compare the DigiKey Bill of Materials to the MS BOM. I created a word document with all the components listed in a table with lots of space for each row. This was to allow me to take the components, still in their nice little sealed bags, inventory them, and staple them to the printed pages (glued to light cardboard) and put them in a binder. This keeps them organized, easy to find and logically labled.
The circuit boards that came from the board-maker that Al and Bruce is top-quality. There's lots of room on the board, the vias and pin pads are very well constructed, and the part numbers and orientation are clearly listed on the boards. It's worth the extra money to buy these items instead of fabricating them yourself, unless you have lots of experience in circuit board building or just want to tackle it.