Yeah, assuming the VTCS is the issue, then I should be able to correct it with the MS. I guess I'm not 100% convinced yet that's what the problem is, and I'd like to figure what's causing it just so I know. Also, Rev's NB2 megasquirts actually control the VTCS in order to help with cold starts, but he has it set to open at something like 1700 RPMs instead of 3500; so if there's an issue with the butterflies being gummed up or something, it may continue to do it even with the MS. I guess if it does, I'll just disconnect it entirely and tune the fuel table accordingly, like you said.

Reviving this thread to post about how I resolved this problem.

The first thing I did was check the vacuum lines for leaks. They were all pliable and fit snugly when I put them back on, except for one, but I replaced it and that didn't affect the issue.

Next, I did every test in the mazda service manual for this issue, and everything tested perfectly fine. The solenoids and actuator were performing correctly, and at this point in the diagnostic process, the manual tells you to replace the ECU. F that, if this ECU comes out, a MS3 will be the replacement.

As a last resort, I pulled out all of the vacuum lines for replacement. Turns out, a plastic Y fitting leading to the VTCS actuator was split, leaking out most of the vacuum.

Check your vacuum fittings and lines!

Did you ever resolve the issue Engi-ninja?

Well, I never figured out what was causing it, but it seemed to go away when it got warm out. Thanks a lot for the update though, if it comes back when it gets cold out again, I'll make sure to check through all my vacuum lines and connectors.

Cheers!