Okay I'm going to try to answer your questions in the order that they were written if the sum of this ends up as a run-on I'm using talk to text. The AFR input voltage's should not have to be changed my suggestion is to ground the wideband and the megasquirt to the same point. If that does not fix the issue then play with the offsets until they read the same in all reality as long as you're within 5% you're okay.
The idle issues that you're experiencing are very common to a new tuner. I don't mean this in a negative way at all I still fight with them most of the time when I'm tuning a car it's really the hardest part 2 tune. I run the same fan setup and when the fans come on the idle does drop quite a bit until you get your settings just right. My suggestion is to set the idle settings too close loop use basic not PID PID can get frustrating. On the slide bar the further right you get the more aggressive the idle air controller is going to work I would set this around a thousand. What you want to do is get your base idle set with the throttle stop then you're going to need to set up your closed Duty and open Duty settings I would set the closed Duty - 10% and the open Duty - 60% don't take this as gospel it's just a good starting point. On the right side of that same screen set your ramp to Target time two three seconds then set your PID control interval to 475 once again play with these numbers until you find what works for you but increasing the PID controller interval will slow down the surging. If you have not setup your idle advanced settings I would try to do that now it's at the bottom of the startup idle drop bar once you're in the idle advanced settings set the idle advance to Adaptive apply as adder and under go to idle Advance when condition is closed-loop PID. In the startup idle drop bar you'll notice the last option all the way at the bottom says idle adaptive Advance timing it's 5 point graph. The middle point should be 00 2 points to the left should be set in a negative RPM Delta the two points to the right will be positive RPM Delta then set your degrees you want to add timing at lower RPM and decreased timing at higher RPM. So if you were to set your RPM Delta - -250 with a degree at 6 then as your timing starts to decrease from your idle Advance set point it's going to add timing up to 6 degrees. This will make sense once you're looking at the page.
Don't worry too much about your required fuel basically that's just a great starting point and all the settings do run off of required fuel it's mostly they're just as a adjustment to all fueling table. So if you notice that you're getting rich across-the-board you can simply decrease the required fuel or increase it if it's a Little lean this also works well if you're getting very large numbers in the fuel table or small numbers at idle.
I'm going to be doing another video here soon I changed quite a bit on my car so when I go to make the changes I'm going to load in an old tune and basically start from scratch this way you guys can see what I do step by step to get a car going