That is a very illuminating picture! The two boards that you see edge on in your first picture, one of which is the A6 Logic Board, connect through to the main interface board (the one about 1cm or so to the left, it carries the four plugin connectors) via a whole host of gold plated pins and sockets. If you look at the A6 Logic Board schematic, <4> in the manual, then there are a run of connectors on the left and right hand edges of the schematic with two letter labels like FA, FS, GG,GE .... These carry most of the signals that are routed to the Logic Board from the plugins, in particular these pins carry the Z axis signal (FQ) and the A and B intensities (FV and FU at the bottom of the schematic). The board, probably isn't bent, just very badly misaligned, either through a ham fisted repair or a severe knock. So it is quite likely that the relevant connectors are on the side that is not inserted properly and have moved that crucial millimetre when you removed the plugin!
Reassembling these board pairs can be a pain since you need to align so many pins at once, Tek made it a lot easier by arranging for the sockets to be slightly oversized at entry and tapering down farther in. If you do decide need to separate the boards, make sure nothing is bent (it is not a disaster if they are, just a good bit more difficult) or broken, and reassemble. It would be very worthwhile to have a look at the corresponding place on the left hand side of the chassis to see if there is anything amiss there that could explain why the left hand vertical slot is not working.
Since the scope was working a day or two back you might get away with just trying to realign the A6 board in place and not worry about disassembling too much. You do run the risk of a moderate bump in future causing the board to move again.
Hopefully you will have a very rare and desirable scope working again fairly soon. Then it would be time to worry about the calibrator issue. To dispel any doubt about the calibrator and how the manufacturers of a DMM have interpreted RMS readings I would just measure a DC supply and see how far the trace moves when you move the input coupling selector between GND and DC.
By the way, the traces on storage CRTs are nothing like as bright as the standard CRTs, they should be very sharply focussed and as soon as the trace starts to broaden turn the brightness down.
Good luck with the repair.