Well that eliminates one problem that would have been a bad problem anyhow as a shock completely extended in a static position is bad mmmkay!
Springs sagging 30mm over time (10 years) is very common, sagging much more than that in standard springs is even more common. Many people who have cars in excess of 10 years old are sadly dissappointed when they buy a new set of 2 inch lower than standard aftermarket springs only to find that their car is the same height or higher because their old springs had sagged so much .
So the conclusion would be that your shocks (short stroke or not) are not making your car lower than standard and the springs that you are running have compressed to a new static height 30mm lower than the standard springs were when new! Or the springs were in fact never going to position the car at the same height as the factory originals?
Good luck with it!
MR2 are awesome little cars, can't wait to see it on the road.