The 400E uses the same engine (M119), so I have some experience with this. First, I'm not really sure why the rubber flaps are there but mine has 'em too.
The thermostat is actually on the SIDE of the housing. I too was fooled by thinking it should come off the top.
RE: temps > 100C, as you know the owner's manual says it's OK, but like you I got tired of seeing those kind of temps, and also the engine computer will retard the timing when coolant temps get that high, so performance goes down.
Do your electric aux fans work? There are MANY, MANY posts on this subject so if not sure, do a search on this.
If they ARE working OK, like mine were, but you are still seeing higher coolant temps than you'd like, a good thing to do is to modify the viscous fan on the engine. There is a bimetal strip on the front of that fan which is set to couple the fan starting at ambient temps > about 107C, so it is really set way too high. It is fairly easy to "fool" it so the fan is on all the time. Stu Ritter (from the STAR) recommends using a small screw and 2 nuts to push the strip out a bit; my tech did it a bit simpler by grinding down the brass ferrule from the top of a spark plug so that the bimetal strip sits higher than the pin. It works really well, and mine never goes above 100C, despite ambient temps of 95-100F.
You'll have to pull the radiator to take off the fan for this mod, however.