I've done a few more hours of reading/testing and I've made some progress. Sorry about posting a bit prematurely, should have figured my first MS install would require some time.
I followed the instructions that come with the MS3Basic to set timing. Basically set it to "Fixed Timing" at 10 degrees, adjusted in Trigger Wizard the offset angle until my timing light showed my 2 timing marks on the crank pulley at roughly "10" and "T".
TPS was calibrated. As for the MAF settings, I am unsure what needs to be changed specifically. I have the "Control Algorithm" set to MAP (speed density) so I am assuming that the MAF in my OEM intake is just being used for IAT readings.
Wideband has been free air calibrated and when used with the OEM ECU made perfect sense. I'm having about a 0.5 point difference between the MTX-L gauge and TunerStudio. I need to rework some grounds or look into adjusting the "Calibrate AFR Table" options to temporarily account for it.
Injector deadtimes was set to 0.9ms. I'm not sure if that's correct but I'll look into adjusting it.
As for my idle problems now, it seems to work fine in "Open Loop" mode once warmed up and after I let the VEAnalyze work with it. I did move the idle screw about 1/4 turn so that the idle is around 800rpm now instead of 600rpm. However, one strange thing is that when I initially followed this guide (Mega Miata: Basic idle settings
) and I attempted to do the "Output Test Mode - Idle Valve", and I'm not sure if my Idle Valve is behaving correctly. After hitting "Start Testing", no matter how many times I hit "Stop Testing" the button never changes back to "Start Testing". In addition, my PWM Idle Duty values start moving at 0%, and go all the way to 100%, which doesn't seem likely. However, I need to keep hitting "Enable Test - Run Position" after each increment.
Also, should my Valve Frequency be set to something lower? I'm setting mine to 204Hz because in another post it was confirmed to be 170Hz, not close to 372Hz as shown in that link.
I'm going to try use this post (Timing at idle - requesting some help
) + the blog post to see if I can get things sorted out.