I'm not an expert in thermodynamics, and I didn't even stay at a Holiday Inn Express, but I'm always happy to share my opinions.
First, with regard to the asymmetric distribution of the temperature left to right across the screen, my guess would be that is because the holes drilled to communicate the water from the "mushroom" down to the screen are drilled asymmetrically, presumably to get the path over to the "infusion device chamber" on the right side of the machine.
I would question the modelling however. From what I have read, the best shots come after the machine is fully heated and you're pulling shots one after another at a practical rate.
In that case, the temp. delta would probably be lower, but whether or not it is, might be beside the point, because it is the water that ultimately hits the coffee, not the E61 housing, so the water temp drop would probably not be as much and (given that it is starting out life at somewhat higher than 203 degrees), it will probably be at or near that (in ideal conditions).
Now, with regard to your other questions:
"Would it help to add insulation around the group assembly?"
It wouldn't help the look of the machine. There is something very tactile about the whole process of making coffee and it's not just about touching the machine (which admittedly is quite hot). But you do have to clean it, and if whatever insulation you chose was not cleanable, forget it. It can't delaminate either--that would be a big problem. Look at the space shuttle.
"Alloy of the brass"
Don't know, but it has a lot of copper in it. I doubt it would affect the model much. Try a few of the most common alloys and you'd probably be fine.
"Flow rate through the Thermosyphon loop"
I've wondered about this myself. I think it is fairly significant. If you remove the mushroom while the machine is on (not while pumping, obviously), you can see it flowing quite spiritedly. If you timed the fluid flowing the first 1/4" out the top tube, you could do the math on the I.D. of the tubing and come up with what might be a pretty good number.
"Diameter of the small duct delivering fluid to the screen"
My guess: 3 millimeters, but it intersects with the larger one above and behind that is more like 4 or 5.
One last piece of advice:
Before you keep crunching these numbers, I hope you've pulled yourself a couple of nice doubles to keep the brain going!