Cat5 cable works fine between the data jack and patch panel, but you can't use pre-made cables to connect
The proprietary IDN connection doesn't really matter; it's just a serial line that uses those dip switches to identify devices. The wiring is straight through so pin outs are easy, the wires are identical on both sides of the cable. Hold up both ends of the cable and compare them side by side; they should match.
You can plug the RJ11 ends into an RJ45 jack, it works fine. If you want to put an RJ45 end on the cable just skip the outer pins and connnect the wires to the center 6 pins.
Try toning out your cable in sections. Remote printer to patch panel, workstation return line to patch panel, then patch everything together with the 1 foot jump cable and see if you get a tone all the way through, from the remote printer to the printer that you're daisy chaining off of. If the cable checks out, disconnect both printers, patch both lines into your switch and try running a laptop or workstation off them. Sometimes there will be an intermittent break in the line that standard testers don't pick up but are bad enough to kill data transfer.