I think you're under-estimating the task at hand;
You had initially said you were going to continue to use the same ECU
with a megasquirt. Now you've realized that the megasquirt is a standalone EMS, but you're still saying you're going to use the megasquirt
with an S-AFC to control the injectors.
I think you need to read before you buy and try things. The S-AFC doesn't touch injectors, it
only affects the intake sensors. It simply alters the reading the ECU receives. You're not increasing mechanical injector flow or anything. Further more, if you have a megasquirt, why would you deal with 'faking out' the megasquirt? It's just more bullshit than you need. That's like saying you're going to buy an MSD Digital SCI but you're also going to run a Jacobs C4. At this rate, you might as well run the 3sgte head with the 3sge head.
People are giving you advice for a reason. Not to discourage you or anything, but simply to let you know that you need to do much more reading before you attempt this.
And for the record, the S-AFC II does not directly advance or retard timing at all. What the case is, is that if you richen, it will allow your car to run full advance, where-as if you lean, it may cut timing due to the fact that it's reading the air as being slightly sparser than it truly is. Running an S-AFC II is not something you should do if you're looking to increase or decrease timing. It's what it is, a fuel computer.
By the way, I hope you're aware that you need to actually make a megasquirt, it's not a store-bought item. With that said, good luck with your build.