I have a 99 Miata with the FMII kit. It won't restart if I turn it off and let it sit for 5 minutes. It'll start right up if I spray starting fluid on the air filter or dump the clutch. Cold starts aren't an issue, and it runs great once it's going. It's done this every now and then for years, but now it does it every time. I've replaced and moved the IAT sensor down into the intercooler. Before it was in the throttle body intake pipe. Didn't help.
1000cc injectors
Hydra Nemesis
Walbro 255 with a return style gas system

Any ideas?

 

Monitor your batt voltage while cranking. Not sure if it’s related, but I did find out recently that hydras won’t work below 10v. Most aftermarket ECUs work down to 8-9v.

If that’s not the issue, have some tools to check spark, fuel, and fuel pressure. An easier test might be just adding ~15-20% fuel in the cranking tables to see if that helps.

 

Well I didn't measure voltage while cranking, but I did just measure the battery before cranking and it was at 12.5v. No start. Squirted a little starter fluid into the air filter and she started right up.

 

This.

 

I increased the fuel in the cranking table by 20% increments up to 100%. Nothing changed. But a squirt of starting fluid gets her going every time.

 

I'll be honest, at this point I would be heavily looking at alternative ECU options. The Hydra ECU is a dead company, with the latest ECU released in 2011, nearly 15 years ago. I consider even the MS3 outdated, having been released in 2013. I do like the Hydra and have tweaked a few tunes on them, but for the most part they're outdated systems with zero support.

I recently spent many hours on a dyno trying to fix a similar Hydra issue, the only fix was a giant battery to keep voltage high, so again, I'd try and monitor voltage at the ECU with a good volt meter and see if it stays well above 10v while cranking.