I just took one of mine apart. The shell (as you know) is held by a single screw under the (steam?) dome. The shell then lifts straight up. When placing it back on the chassis, it goes straight down.
As I mentioned, maybe the circuit board or the topside wiring is interfering? Here are few of photos, similar to the ones I used in the N-Scale Magazine article.

Bottom image is unmodified chassis as it came from the factory. Notice that the white wire's insulation was pinched at the screw area (the red is also slightly pinched), and more pinching is evident immediately to the right of the electrical tape (the front of the brown motor cradle extends too far up). I cut of the very top of the motor cradle to make room for the wires.
The top image is after I cleaned wiring and seated the wires in the channel molded in the chassis. But the channel is not wide enough to hold all 4 wires (when the extra 2 wires are routed to the top. I had to widen the channel slightly to accept all 4 wires.

The rear circuit board.
On the right is unmodified board installed at the factory.
The right photo shows it after I cleaned it up. I replaced and re-routed the wires goinig tot he tender, and cleaned up the wiring on the top.

Also make sure that the valve gear is not interfering with the shell.