Hello Reece,
I had a similar issue on my NA after having clutch work done.
The noise is now almost completely gone and much improved. I’m guessing the principles are much the same, but I will leave others with NC knowledge to fill in the gaps.
Speaking to an MX-5 specialist he said always take the measurement of the PPF before starting any work and to put it back in the same position. I know this is true for the NA and NB.