My MX5 donor appears to have a front to back split braking system, but I know most modern cars come with a diagonal split system. Is there any issue with sticking with a front to back split, or will I have IVA troubles?

Most cars running two master cylinders are split front back - so in short no.

Front-rear split is the normal way for brake plumbing on a Seven style car anyway.

Awesome, thanks!