The first step is getting the motor out. The best way if your doing the engine and transmission is to undo the subframe and lift the car off the engine, transmission, and suspension like so:
Once the assembly was pulled from the car, it was separated from the subframe, the subframe was bolted back into the car so the car could be rolled around.
The engine was put on a engine stand and disassembly started. Care was taken to take photos and label parts as they were removed. Plastic bags were used to keep bolts and things.
The electronics and harness were removed. Then the intake manifold, alternator, starter, ac compressor, power steering pump, and pulleys were removed. The heads were then removed and set aside as new heads were to be put on.
Here is a diagram that may be useful:
Keep in mind when using the megasquirt msII nearly all the engine sensors will be replaced with GM ones. General Motors parts are cheap and readily available.
For the actual build, we are going to need to find a temperature controlled environment to check all the dimensions of the pistons, block, ect prior to assembly to ensure there are no quality issues with the newly machined parts.