My Megasquirt adventures over the years
These next two are probably some of the most important settings and ones that I think a lot of people don't properly account for or understand, the Air density and MAT/CLT correction curves:
I mentioned this in my original post, but the air density correction curve especially people seem to take a lot of liberties with. In my opinion, I don't think they understand the physics of the situation and they use it as a band-aid. Actually, you can see in my screenshot I'm guilty of using it as a band-aid at the moment as well, though I'm planning to try to remedy that. I believe the long version of the story is that this curve used to be hard baked into the code, but people were having issues with heat soak and other things, so they moved it out where it could be modified. I think the biggest thing that drives people messing with this table comes down to sensor placement. What the air density curve is doing is modeling how the mass in the intake is changing as the temperature increases and decreases. As the tool tip and text above the graph state, in theory this curve should follow the ideal gas law. Where I think a lot of people have issues is that they think the air temperature they read at the throttle body is the same temperature as the air that is going into the cylinder. There is a chance it could be, but more than likely you are going to see some heat rise between the two. I think I actually got lucky with this one, because I have my MAT sensor in the intake runner right above the intake valve (I don't have the six pack top plate, but same base):
I'm using an open element style sensor that changes temps pretty quick due to low thermal mass:
You can actually watch my MAT values rise and fall with the TPS signal while I'm cruising down the highway in this datalog:

The yellow trace in my TPS and the white trace on the bottom chart is my MAT. It goes from ~80 degrees on the left to 90 degrees or so at the peaks in the 20 seconds I rolled off the throttle, then it starts dropping back down as I get back into it. If I sit at a stoplight or in a drive thru or something I can see my MAT values hit 180 on a hot day, and I have a hood scoop and 360 degree air cleaner with flow through lid (though it's not sealed to the scoop, something I'm looking at fixing one of these days).
So my soapbox sermon of the day to all the people that say to zero the air density chart when first tuning your car is "don't, at least not at first". The chart is there for a reason, and the ambient temperature is only vaguely related to the actual air temperatures inside your engine. In my experience on my setup (aluminum intake, hood scoop, my particular air filter, etc.), the MAT values I see at my intake runner while cruising down the highway tend to be ~20 degrees warmer than the ambient air at minimum. With more intake vacuum (throttle closed), they tend to rise because there is less mass in the intake, so it takes less energy to increase the temperature. That's not saying you can't tweak this table, but do not zero it out. What you should probably be adjusting is actually the MAT/CLT correction table. That one more clearly describes the issue going on if you read the tool tip. It basically says as air flow goes down, assume the temperature of the air entering the cylinder is closer to the coolant temp than the ambient temp. Conversely, the more airflow you have, the closer it would be to ambient. I see this first hand on my car and am planning to try to play with this table in the near future. I have an issue where my car tends to idle lean, but runs normally once I start driving. I've tried adjusting the VE table to richen up my idle area, but then it's way too rich on first startup, so it's a never ending fight. I'm pretty sure this table is the solution to that, I just need to figure out the values. Okay, rant over.
HP Tuners has similar tables for reference:
I think they are a little less clear on the surface, but I have tried to use some of them on my setup. They split it up into two tables each for CLT and IAT sensors. Each one gets a table for RPM vs MAP and a table for a multiplier based on the direct sensor reading. The IAT table is all ones for RPM/MAP, so it scales purely off of the IAT values. This would be similar to the air density correction curve in the MS. In fact, I actually had these values in my car before today and may go back to them, depending on how my tune adjusts to different weather. I think their values may have some of the heat transfer of the intake built in and may account for the IAT positioning. They used a plastic intake with a sensor around the throttle body I believe, compared to my aluminum intake with a sensor in the runner, so time will tell. The coolant table is interesting because it does care about RPM and MAP, as well as scaling off of the CLT sensor on top of it. The CLT scaling table we'll look at later when we get to the startup/warmup section of MS tuning as I believe that is effectively what these values are. The RPM/MAP table for coolant I believe has a parallel in the MS MAT/CLT correction table, so I have some work to do to see if I can translate those values over. Interesting that table ends at such a low rpm though.
Probably enough for one night of rambling...