nice going!!
I have begun to calculate dimensions based on both my own in-person approximations and the pictures I have.
At the Backlot tour, I've often paced out how long the "barrel" is, and I'm using 5 feet as a good standard approximation (we'll never be sure until someone can get through the mesh that guards the machine and use a tape measure).
Based on a 60" barrel length, I've come up with the following measurements:
The diameter of the 8 copper tubes that comprise the barrel (7 around the perimeter and 1 in the middle): 4"
Gray cylinders that make up the emitter: 5"
(when I used the 5" approximation on the dead-on screen shot of the machine, it produced the following exact measurements which I think are close to accurate):
Nose cone diameter: 3"
beam opening: 1"
There are two black squares that section off the machine.
They appear to be approx. 5.5" wide. The back one extends downward slightly farther than the front one, because it attaches to the heat sink directly with a kind of L bracket, rather than via a little square piece like the front one. I'm pretty sure the front one is close to 5.5" square, and the back is 5.5" x 6.25", based on my measurements.
The little box on top that houses the stablizing rod is 1.5" x 1.75", and the stablizing rod itself is 3/4". I used the 3/4" assumption to glean ALL of these other measurements, and they all fall perfectly into place. I tried them with an assumed stablizing rod measurement of 1", and that made everything else way too big. Plus you can clearly tell from screen grabs that the stablizing rod is not 1", which is the ghostbusters proton gun handle size (one gets used to how big that looks after building 7+ proton packs!)
I've seen the machine in person, and it's possible to walk astride it and estimate it's length that way. There is simply no way it's longer than 5 feet. When you doubt yourself and think you're making things too small, remember that the screen always makes props look bigger than they are, especially in this case.
I think you should keep going with your nose cone, even though you said yourself it was slightly too large, because the alternative is to machine a perfect nose cone and we all can get that PVC piece. It looks great so far!
Capacitors come in mm, and using the Nose cone estimation I came up with an appox. dia. of .9 inches for the capacitors, which is almost perfectly equal to 22 inches, one of the largest ceramic disc capacitor sizes.
Likewise, I used the 3/4" stablizing rod measurement to come up with the following measurements for the heat sink.
It's about 15.5" wide, with a base of 1" and 3/4" fins. It's approx. 26" long. I'm guessing the guy who built it (I can't remember his name ATM) went to a surplus house like APEX and found a bunch of stuff lying around. No telling where the heat sink originally came from...
I'm making a new rendering in sketchup based on all of these fresh measurements (I did the one in anim8or back in 2007). Here's a glimpse:

I'm going to use the new rendering to create plans.
About the gear situation:
I always imagined basically fabricating an approximation of the gears and scissoring arms, and mounting it on a black metal arm so that you couldn't tell it wasn't functional...maybe this is the best course? Unless you're an engineering wizard in which case help me/us?