Hey everyone,
I’ve got a ’90 Miata with a built BP4W swap that I recently turbocharged. It’s running on Megasquirt PNP2 for engine management, with a Skunk2 intake manifold and throttle body. The problem I’m running into is with high idle:

• Cold Start Idle: ~1400 RPM
• Warm Idle: 2000–2300 RPM

What I’ve Tried So Far

1. Smoke Testing Intake System:
   • Found and fixed all leaks.
   • Verified with soapy water—no leaks detected now.
2. Throttle Body Adjustments & Replacement:
   • Adjusted throttle body stop screw.
   • Replaced the Skunk2 TB with a new one and even swapped in a stock TB—no change.
   • TB is closing properly, I aggressively set the preload on the spring
3. Replaced IACV:
   • No improvement.
   • Tried running the car without the IACV; it won’t run without it.
4. Intake Manifold Work:
   • Pulled the manifold, replaced the plenum gasket, applied a bit of RTV, and reinstalled with an OEM manifold gasket.
5. COP Conversion vs. Stock Ignition:
   • Reverted to factory ignition, reset ignition timing (it was a bit advanced).
6. Idle Advance Adjustments:
   • Disabled idle advance in TunerStudio, which helped lower idle somewhat, but it’s still ~1400 RPM.
7. Injector Seals:
   • Ordered new seals as a precaution (current ones are new, but I want to rule out any vacuum leaks).
8. TunerStudio Adjustments:
   • Set IACV duty cycle low: causes surging until the engine shuts off.
   • Incrementally increased duty cycle until surging stops, but the idle remains high.

Current Status
I’m at a loss. This issue has been super discouraging, and it’s holding up progress on the rest of the project. I’ve attached my tune below and am open to any suggestions to get this sorted.

Has anyone dealt with a similar high idle issue? Any advice would be greatly appreciated!

 

I'm surprised in that whole list you didn't mention anything about tuning.

Is this a new problem that used to not be there? There are a few settings that are pretty weird in your tune, maybe that's you trying to fix the high idle, maybe it's the cause.

Try the attached tune, and see if it's any better. Feel free to browse through the changes I made when it pops up with the "differences found" page. Long story short, idle advance was increasing timing a bunch, 20+ degrees, which would actually increase your idle. Idle valve hz was also a little high. Take a data log of it idling with this tune loaded, and post it here please.

 

In addition to curly's point, the stoich AFR is set to 14.1, but the targets are still following the 14.7 scale. I suggest setting stoich AFR to 14.7 to remove confusion. As it is now, the ECU is attempting to idle at 15.3 AFR, and high boost is in the low 12s...

 

I think I was assuming this was a new, untuned install, mainly looked at idle stuff, so yeah, don’t forget to tune the rest.

 

So the car wouldn't start with the tune so I increased cranking IACV duty cycle and changed the CL Idle PID Gains tuning mode back to advanced. I am hoping that log is good for you, I started it about a minute or two after initial start and it began to idle at 1300 and at 1700 after 2-3 minutes

 

Most likely the lower hz needs more start up duty. The PID settings only take effect when it enters CL idle, not starting. But unfortunately, you attached a composite log. Take a datalog by pressing ctrl-L, name it something, press enter, once done press ctrl-K, and attach it here.

 

So I ran your tune again, no changes besides increasing IACV frequency and it started no problem. It has a 99 IACV if that makes a difference

 

Ah shoot, missed that you were in fixed advanced. I fixed that, went back to 313hz (that's closer to what you want), and added 10% cranking duty so it'll hopefully start. EGO was also doing more harm than good, so I turned that off again, and let your idle valve go to 0.

So feel free to try the attached tune. BUT, your running voltage is way too high. You should really fix that before moving forward. Most of that log was at 15.75 volts. Ideally it should be 14.5 or lower. IIRC, the MS2 has a fixed alternator control circuit for NB alternators, unlike the MS3 that has programable target volts. This circuit may be fried on your MS2, or you could have something wrong with your alternator/wiring. I'd start by getting a known good multi meter and checking resting and running voltage compared to what the MS is seeing. Best case scenario, your calibration is off and you can continue diaging the high idle.

 

It's also important to note that idle valve frequency is not a tunable thing. There is one frequency that works well, and everything else won't. Ideally your valve will work in the 20-80% duty cycle range. Below 20%, RPM won't continue to come down. Above 80%, rpm won't continue to increase. If your frequency is too low, your idle valve will barely increase RPM. If the frequency is too high, it'll jump from closed to open within a small window of duty cycle. Miata idle valves operate best around 300hz, hence why I turned it down from your original 480hz.

 

Yeah I noticed the voltage was high, luckily I am a tradesman, so I have accurate multimeter, I will test that tomorrow for the sake of my neighbors. But I ran that last file and it idle at 2000rpm. Also, I am running a Fluidampr Harmonic Dampener, I am not sure if that would mess with the amount of times the alternator would spin as the Fluidampr is considerably small than stock. My concern that this is a mechanical issue, but I've checked everything, no vacuum leaks, I've smoked the intake and found nothing. Anything else I could be missing?

 

Any chance the throttle cable is too tight? Have you messed with the bypass screw? After you double check voltage, if it is ~15.8, maybe remove the alternator belt temporarily and see if that changes anything. That’s your water pump too, so don’t run longer than ~20 seconds. If it’s still high, I agree it’s a mechanical thing. After that I’d be looking at a OE manifold to see if that fixes it.

 

SO, update! So voltage was fine,reading from battery terminals I was getting a reading of 14.38V. So messing with the battery calibration in TS(because I don't understand how it works) I started lowering the voltage and telling the ecu that the battery voltage is at 9v-ish my idle begins to lower! Would you happen to know how I am supposed to change the two values so it calibrated and how should I mess with the PWM voltage compensation to get it to idle at target.

 

Did you swap alternators when you installed the MS? That might be your whole problem. You need to install a 94-97 alternator if you're currently running the BP4W alternator. That one is ECU controlled, and I don't think the 90-93 MSPNP has the circuitry to control it, and it definitely isn't wired correctly without physically changing it.