I also agree that the car is geared way too short! I have owned 3 MR2 NA's with 5 speeds over the years, and I always dreaded interstate driving. I would even make a point to use secondary highways instead and therefore stay at 55-65 mph...But even then, I would be zinging along at 3000+ rpms, and people thought I was some dork wanting to race their minivan or Taurus when they would hear my car zinging like I am in 3rd gear. Cruise control was jerky too, due to the revs, and a road trip was out of the question...
I have recently purchased an automatic MR2 (91) and to my surprise it is geared very low by comparison. For example, it runs around 3100 @ 85 mph (the official published figure is 2200 @ 60). Gas mileage is incredible too...basically think of it like a lightweight 4cyl Camry when it comes to fuel mileage...I average about 29-31 mpg in mixed driving, and easily make 40 on the highway.
I initially bought it as a project / daily driver, but really started liking it the more I drove it. Normally I would never want an automatic in a sporty car, but I found this to be an exception - probably since it has a Camry motor anyway, and has all of its power toward the bottom and middle of the rev range. It really just feels like the engine was designed to be mated to an automatic, which is more than likely considering how many Camrys were sold

.
But then again, I understand that some people won't drive an AT no matter what, so to each his own. Also, I am sure you guys in other countries that have the "hot motor" MR2's would probably think I am nuts, but really you would just have to drive one with the 5SFE motor to understand, and there are so FEW with automatics here that it is rare to even see one, much less compare one.
If our MR2's had the engine you guys have, then it would be a different story, and the tractor gearing and 5 speed would make more sense, as it does in the first generation MR2 - the more revs the better.
Anyway, back to topic: I wonder if it would be possible to swap the diff out of the AT MR2 or possibly from a turbo MR2 (I am sure they have a taller diff.). Heck, for that matter, I would think any given Toyota diff would be taller than the NA, for example a Celica, or Camry? I would love to try a taller ratio in my 5 speed...
One more thing we must consider...we would also need the speedo gear from the donor car.