3-way switch tied to box, one switch removed, can't make sense of it
Going three-way with a relay

In order to have a normal three-way switch between the two locations and have receptacles at the far end, you need four wires (plus ground): a hot, two travelers or a traveler and a switched-hot, and a neutral.  Since you only have three wires, and can't really replace the cable between the two boxes, you need to do something else here, as the way it was working (using the bootleg jumper to use AC armor as a neutral) was shockingly bad.

There is an alternative though -- a device called a relay, which acts as a switch that can be remotely controlled by an electrical signal.  In particular, we'll be using a RIBU1C from Functional Devices: this is a SPDT relay that can be controlled using either 24VAC from a transformer or 120VAC from the wall, using an on-off signal to determine which position the relay is in.  Thus, we can use the SPDT contacts of the relay as a 3-way switch that's controlled remotely by a single-pole switch somewhere else, using only an always-hot to the switch and a switched-hot control wire.

In your case, I would install the relay at the far-end box (where neutral is present), then repurpose the wires in the existing /3 AC cable as follows:


Black -- always-hot.  Leave it as is.
Red -- relay control feed. Leave it attached to the near-end 3-way switch, but unhook it from the far-end 3-way switch, as we'll need it when we install the relay.
White -- neutral.  Connect it to neutral at the far-end box, and to the receptacle neutral at the near-end box, unhooking it from the 3-way switches at both ends.


This means that with the bootleg jumper gone from the near-end box, we now have a situation where the 3-way switch is acting as a single pole switch, so that it can turn the relay coil on and off.  Once all this is done, the far-end box is fitted with a RIBU1C (mounted to a 1/2" KO on the box somewhere), and the RIBU1C is wired as follows:


White/Black -- to the Red wire from the /3 cable
White/Yellow -- to the neutral wires in the far-end box
White/Blue -- capped off (unused)
Blue -- to one traveller screw on the far-end 3-way switch
Orange -- to the other traveller screw on the far-end 3-way switch
Yellow -- to the always-hot wires in the far-end box


As to the ground at the near-end box? The armored cable's armor provides something of a grounding path -- old armored cable is no longer current Code in this regard, but it's better than no path at all, and if it's type AC with a "bonding strip" wire under the armor, then it is fully Code-compliant  as-is.