Trial and error from many owners experience on road and track. I don't know how much lighter the mx250 body is over the mx5 but you know what the originals were, you know you want them shorter, so not too difficult to guesstimate. Likewise with a spit/herald based kit - there's years of experience out there - you just have to take the lighter weight into account.
You can buy decent adjustable kits but much cheaper to get fixed length. What you need is friends who race and have piles of springs in their garage for you to try