Aside from my 3/5 Metro, I also own a 2000 MR2 Spyder.
When the transaxle pinion bearing noise got real bad (common problem with them), I swapped out my old 5th gear for a new taller one out of a Corrolla (I have the part numbers around here somewhere). I haven't done it, but it looks like you
could do the gear swap with the trans still in the car. Otherwise, it's a 10hr job for a non-pro like myself, floor jack and stands, to R&R the trans. Removing the front cover and the gear swap itself is straight forward. RPM's in 5th dropped by about 500rpm, perfect for freeway cruising. My fuel economy improved by about 4 mpg on long Interstate trips as a result.
Unfortunately, those early 3rd generation Spyders are notorious for their rings wearing out prematurely, and burning oil. (Check Spyderchat.com if you haven't found it already).
Far outweighing aero improvements, this will be your biggest challenge toward FE improvements, as burning oil causes engine knock, which sends the ECU into ignition timing retard mode, lowering both power and FE. A bandaid for this, is to use Premium fuel.... ask me how I know
I now have an oil separator in line with an aftermarket, CARB approved, high-flow PCV valve that works to combat this issue. After a couple of close calls with low oil level, I installed a Moroso extra capacity oil pan, reducing my chances of accidentally running it out of oil (I drive 700/week). I'm back to burning regular 87 octane fuel since adding the separator. It's been a good strategy so far, I now have 200k mile on the odometer.
Anyhow, the 'behind the seat' factory flip-up wind deflector does work, I have seen people replace the factory plasic with a taller one, that reportedly reduce wind noise (my gal doesn't like her hair wind blown, so I'm considering this option as well)
As you probably already know, factory hard tops were available in Europe for these cars. There is a guy that imports used ones to the states for about $2600 incl/freight. That would be a great foundation from which to start modding the 'greenhouse'.
If you are really serious about FE, I'd reduce rolling resistance. Consider dumping the wide performance tires, opting for a different rim, narrower, with LRR tires, and reduce the rear positive camber. You can disconnect the electric power steering easily enough. Unless you are a girl, manual steering effort is not bad at all, even at low parking lot speeds.