A fellow MR2 owner here. The wing is definitely not stock on your car, woodsmith, but the sides are. From what I've experienced, if you don't want to remove the wing because of the holes, but don't want to keep your current spoiler for drag reasons, find a stock one. The wind barely hits it (rain drops and especially snow sit on mine even at 60mph). Just for reference, but there were MR2s without spoilers available, as there are used OEM trunk lids out there without holes in them.
As far as the rest of the car, there are 2 major aerodynamic issues:
1: The rear, especially where the back window and engine lid are. There is very little flow up through the vents in the lid, so the air from above just dips in and slowly swirls around in that area (causing annoying water spots after it rains, since the water just sits there). That's why the air never really reaches the spoiler in the intended fashion. Add a vented lexan panel over that area (add venturi tabs at the end of the roof for bonus points!), and you'll probably see enough airflow at the spoiler to start thinking about removing the spoiler.
2. The front end. Since it's a mid engine car, the air basically flows through the radiator and slams against the front trunk firewall, then gets shoved almost straight downward, instead of flowing through the engine bay to the back. That, coupled with overall poor stock underbody aerodynamics, can actually create lift at high speeds from all the turbulence. Many people have complained about that throughout the years, a feeling of the front feeling floaty and disconnected on the freeway. The car can definitely benefit from a front and rear end underpanel to smooth things out. There are also what are known in the MR2 community as "Speed Flaps". They were available on MR2s in Japan, but never made it over here. They're the deflectors that you see under many cars today in front of the front wheels. They significantly reduce front end lift at high speeds. You can find replicas at Brady Motorsports.
As far as the radiator, if you're looking to sink some cash into this, you can tilt the radiator forward, cut a hole in the hood (or get a vented aftermarket hood), and vent the passing air out over the hood. That's the most aerodynamic way, and will significantly improve the front end's faults. A company called Border even sells a conversion kit.
Beyond those two issues, there really aren't any other unique problems as far as aerodynamics. The usual mods shown on this site will work, though they won't make your car look any prettier.
Check out MR2OC.com, the biggest MR2 site out there. You need to register first to view anything, but there's a wealth of information on anything MR2 related you need.
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