For the guy that said that missing flaps couldn't cause overheating. I have done some reading on this, and I would be tempted to agree with you but here are some ways it could cause overheating:
1) the holes that are left in the fan shroud allow air to flow improperly. If you know anything about the bernouili (sp) principle, you know that air can do weird things when you are traveling at road velocity. That's why you need to have your decklid closed. It seems logical that an open decklid would provide better cooling, but the argument is that at road speed the air actually ends up sucking OUT of the engine compartment, which causes more hot air from the engine to get sucked into the intake for both the fan and the carb.
2) Your cylinders never get cooled properly. They run hotter. Your engine now has more of a temperature differential between the case and the heads. This can cause problems due to the thermal expansion properties of metals (of which there are several kinds along the line from the case to the heads).
3) In my case I think I am also missing a vital piece of tin at the top of the cylinders, intended to deflect air over the fins instead of straight down through the middle. I don't know for sure yet if this is part of the flaps assembly that was removed but if it is it fits in the "keep your flaps" category.
I have noticed, although I'm not yet positive, that my temp rises mostly only at highway speeds. If I'm cruising around town in 3rd gear (35mph-1500rpms) it doesn't seem to heat. But on the highway in 4th (70mph-1500rpms) it does. This would point to an air leak problem: IE my engine compartment is not properly sealed (maybe those flaps holes in the fan shroud) leading to hot air from below coming up and being recycled over the cylinders.
I tend to agree with the folks that say that VW spent a lot of money with the best engineers and equipment they had (albeit early equipment) measuring temperatures all over the engine in a variety of conditions. I'm pretty sure they didn't put the flaps on because they seemed cute. I'm pretty sure that they did it because they were having a problem and they were trying to solve it. Although they could have made a mistake, if I were to put money against me and the top VW engineers of the 60's I think I'd have to put my money on them!!! That's my take at this point. I don't claim to know everything but some of what I have read does make sense and even if it is not causing my extra heating it still sounds like a good idea to get those flaps back.
If nothing else, the flaps should heat the cylinders more quickly during warm up which would decrease wear, since without them the air is spread out over both the cylinders and the heads.
That's my contibutory two cents after reading up on the matter for several days.
By the way, I think you can still get a Mexican thermostat and from what I've heard they work fine. They aren't OEM for true classic show cars but other than that they should be a good option.
Chronologic