Here are the details about the rest of the enclosure. The case is designed as a sandwich of 3 PCBs (the main board, front panel and the frame holding LCD) and two 3D-printed plastic parts (back lid and spacer between the main board and front panel). All the parts are held together with six 6-mm M2 standoffs and 12 flathead screws.

From bottom to top. Here's the 3D-printed back lid designed in OpenSCAD. You can see a hole for the reset button, an opening on top for the ST-LINK programmer connector, and six slots for standoffs.

Main board (the reverse side opposite to the switches). The change with respect to the first revision is the use of the Keystone 1057 coin battery holder, which sits in the cutout of the PCB and allows the reduction of the thickness of the whole thing. The total thickness of the enclosure is 9 mm compared to 13 mm for the old version.

A spacer between the main board and the front panel is needed to position the LCD and the keys at the correct distance from the switches.

Front panel PCB with silkscreen labels (0.8mm thickness):

The frame holding the LCD was originally planned to be made 3D-printed, but I found out that it needs some rigidity, so instead I've made an ad-hoc one from the remaining front panel.

Here are a few photos of the guts after soldering. 3D-printed spacer with the front panel attached and key "caps" visible through the holes in the spacer. The LCD is also inserted: the back of it is visible through the battery holder hole, and its flex cable. You can also see the hex standoffs sitting in their holes.

Same with the main board added on top: 

What's that black tape mess, you ask? Unfortunately, it appeared that one of the vias on the PCB had been defective, so the whole column of keys was not working. I had to solder a wire directly to one of the STM32 pins and route it to the opposite side of the PCB. The other four PCBs in my order seemed to be OK (at least, this particular track), but I was too lazy to move the already soldered parts to another PCB given that this revision is anyway not a final one.

Finally, the calculator fully assembled: