My Miata (or MX5 as their known here in the UK) is a 1999 (mk2) 1.8iS - not sure what that equates to in the US

That should roughly equate to this diagram. On page 10 (engne performance) I find three wires that I'd check for the right signal. You can also cross-reference that with pin-layouts of your computer (miataforum.com should be able to provide you with that).

but im just wondering if that speed sensing wire is in the factory audio harness somewhere...

it was in mine, but I had MSSS. I don't think your harness has it, if you didn't have ALC.

or is it a seperate wire? if not then do you know which pin on the connector it is?

The link in my last post contains the pin-layout for all MPSS or MSSS model radios in the US miata. That's where I found my wire.