Hey yall,
I'm just making this post so anyone who searches or doesn't, do the same as I did. With MSPNP pro, I managed to short the 5v ref to ground (no load/PIN H) therefore managing to pop the 500MA fuse inside it.. Therefore, what I am assuming is to lose the rpm signal as well, making my miata not be able to run until the fuse is replaced WITHIN the megasquirt. Yup.
TLDR: Don't short the 5v ref to ground.