I am not sure what John did with the output files. I suspect he is keeping the extension of whatever the input file was. The _MOD is the hint as to the newly saved file. Renaming the extension to the appropriate device is allowed and necessary.
There are a certain number of lines that are unique to Cube3 and CubePro. These are the park, wipe, and other commands that do the housekeeping. These have to be valid segments. Using an appropriate header from a pre-generated file from the proper platform is a good way to get the information. The 'body' of the print only uses a few commands. This is your slicer proper.
I don't know anymore what the M404 was. If it isn't found in .cube3 files then yes, delete those lines.
We've covered a lot of territory in this thread and I am certain a lot of good detail is buried among the rubble. I think John did try to add some information in the help. Not sure how far that got.
Your assumption is correct - the editor was a tool to simplify conversion from Cube3 to CubePro and visa versa. The hooks are there but the differences but implementing a complete conversion would have quadrupled the effort. I'm not sure if John has continued this further on his own. I heard he was customizing on contract. The editor's settings are made to change the two parameters that don't work identically between the two machines; pressures and speed. Temperature is an optional setting, mostly implemented for various material combinations.
I have a routine that changes Ekocycle prints to Cube3-abs prints where I run PETG from the spool;
1) Load the .cube3 file
2) Increase the pressure of the first two entries to manage the extra gap assigned to Ekocycle prints
3) Change 265C to 250C in all locations
4) Change to Cube3 header data (left pane)
5) Pick an ABS color currently chipped to my cartridge
6) Save Cube3 file which assigns _MOD to the original name.
Link me up with a CubePro and Cube3 file you want to use. Single color is pretty much a limitation for this combination. Ever filament change operation is a huge manual effort. Anyway, I can see what can be done with those and get them back to you. Also, which way are converting - pro to 3 or 3 to pro?