I'm not using the stock manifold, so where I have mine doesn't matter :)
If you can, stick with a PWM idle control valve - the stepper motors (in my experience) are much harder to tune, and get to behave consistently.
For the coolant temperature sensor, just remove the existing thermotime switch. Then drill out, and tap the existing adapter to fit the new coolant temperature sensor.
Just use GM sensors for everything. That's what Megasquirt plays most nicely with.
As for the product differences, you should really read the documentation to learn about the different systems. A lot of the questions you are asking are already answered there. Read the docs, and get to know them inside and out. This is complex stuff, you need to know the documented basics first. You can find everything at:
http://www.msextra.com
Poke around and read everything on diyautotune.com. Pretty much everything is already answered between those two sites.