Help needed! SEI DT router 650.

If it takes HP-GL codes from the serial port there is no reason it couldn't take them from a Linux machine.

I have written software (in Gnu octave) which controls a Roland plotter this way. In my case I was using a Mac and a USB to serial convertor and the Octave code was used to slice an STL file and cut out layers to build up a model.

You can probably drive your plotter from a serial terminal application, just typing HP-GL codes. I can't remember many of them at the moment, just PU for pen up and PD for pen down. It's a very simple language though.

EMC2 is not likely to be much help with the machine configured as it currently is. EMC2 converts G-code into motor movements. Your current machine has a built-in system that converts a different language into motor movements. To use EMC2 you would need to replace all the current "intelligence" with EMC2.

It is possible that the current system has individual servo drives for each motor. If that is the case then you would need to remove the current motion controller, and connect EMC2 to those drives instead. If the power electronics are integral with the motion controller, then things are rather more difficult.

A Z80? Wow!

What numbers are on the devices bolted to the heatsinks on the middle board?

What you have is effectively a printer. HPGL is a printer/plotter control language and with the right (generic) drivers you ought to be able to simply print to your engraver from any graphics package. (Best results will be from vector graphics software).
A quick Google suggests that Inkscape will output HPGL.

Alternatively, if you want to control the machine as a CNC machine using EMC2 and G-code you are looking at a complete retrofit, replacing the motor drives and controller (but you should be able to retain the motors and encoders).
Deciding the best way to retrofit does require knowing what the motors are (stepper or servo). The fact that I see 4 tracks to each motor on the backplane makes me suspect stepper, but one could easily be an earth.

Put a sticker/label on that chip with a window in it. That's an EPROM, and can be erased by UV light.