Prototrak Plus Retrofit with Mesa 7i77 & 5i25 cards

Well, you will have to fix more of those errors there, plenty more to go.
You have to use the replace function for doing such editing, and you have to keep track of what is changing and to what and how that change effects the other parts.
You can learn that in half hour, and it will save you a lot of time later.
Back on topic.
You still have to fix things like
You have scalemax and scalemin to analogout0 and analogout 1 as output for the same axis. That will not work. Same thing with limits and encoders.
It is much easier to do a new config, and place the connectors on the 7i77 in the coresponding places.
I do not understand why you change and edit hal to switch places, just unplug the connectors on the 7i77 and plug them as they should normaly be.
Even after this you will have to edit a bit, but very litle. And use the "replace" in gedit or mousepad or whatever text editor you are using.
Do not use replace for replacing 1 with 0 or similar short things, never.
Select a long part that is the same in all the lines you want to replace and just replace with the same thing plus changes.

Use google and type / linuxcnc "servo tuning" / with quotes, without brackets or slash, you will find a nice tutorial by JT and another one that deals with FF1 and FF2 setings.
Read them properly, understand everything, use hal scope to get a grip on how to set it properly, and it goes quite easily after that.
When tunimg, changing values for PID requires a lot of patience, changing P value is easy, everything else has to be done with smal increments following the scope to se how the feedback behaves and noticing smal changes in f error. One example i had lately, i got it quite close to perfect with a FF1 of 0.03 but not quite there, 0.02 much worse, 0.04 worse, 0.031 worse, 0.029 worse, so i went from 0.0301 and when i set it at 0.0303 it was smooth as silk. That is an example, on how sensitive some combinations can be, and without hal scope, it can mot be done.
Also as soon as you get motion, try to set the scaling exactly right, use a bit of load to check if tuning can follow properly when loaded, check different speeds, etc etc.
Just use caution when enabling drives so you do not get a run out, and follow the dro, if it keeps counting something is usualy set reversed, .......
Plenty of fun to come, for sure.
And do not enable all the drives at the same time, 7i77 has detachable connectors, so only 1 at a time till you get that all tuned, then move to the next one.