Configure scara robot

Should go something like this:
Make a config for joints/axis you have with the correct pins using StepConf, start that config and check if everything moves correctly.
Since you have opened the scara sim, it's config folder should already be copied to your /home/whatever_name/linuxcnc, so copy the .hal file from the stepconf created folder to the sim folder.
Open both .ini files (from sim and stepconf), select and copy from stepconf to sim .ini everything reffering to axis/joints.
Near the top of the sim .ini find reffernces to sim files and delete them and add the .hal file name you copied from stepconf to sim.
Save everything but do not close the text editor, try to start the sim.
If everything was copied correctly the robot should move now.
If not, see the "debug" section of the error report and fix whatever is missing or duplicated, save and try again.
Do not close the text editor till you get things working as it is easy to go back with "undo" in case of typos.

Usually the vismach hal file has nothing to do with the parallel port, all it does is create a graphic rendering and connect values like the joint positions to that. As such vismach is not required for a working configuration at all.