It sounds like you are on the right track. Since I'm a self taught megasquirt tooner, I'm an expert at it....lol. Here's my $.02
Set your timing like a mechanical advance distributor. Get your AFR where you like it across all scenarios. After that's all set, adjust your timing. Timing does not affect AFR. I tried the "vacuum advance" cruise timing at 40-45 degrees and I didn't care for the way it made my car run. I honestly don't see any benefit. I have individual coils for each cylinder so I can pretty much dial in whatever advance I want. My motor like "all in" advance around 3200RPM. I just keep it there based on RPM, not MAP.
I've never tried the auto tune in Tuner Studio. I've read so many posts where it made fuel tables a big mess. Therefore, I've stayed away from it. (Holley auto tune is a different story).
Here's how I tuned the VE tables and it seemed to work pretty good.
- Go for a long drive while data logging. Drive it hard in every gear multiple times, cruise for a while, sit in traffic, etc. (ride the brakes to get into cells that are outside of normal driving)
- Load your log into Megalog viewer and set up the Histogram/Table Generator to have the same X & Y values as your VE table. MAP on Y and RPM on X. Select AFR on the Z axis. It will automatically show your AFR in the cells and you can see where you are rich/lean. Do some math and determine what percentage you are high/low from your desired AFR and adjust your VE table accordingly.
- Repeat this process until you get your desired AFRs when you are out cruising. It only took me a few times to get it really close.
If you run closed loop AFR control, you will notice it runs much better when your VE it close to the target because the software isn't working as hard to make corrections.
What throttle body are you using?