Please help, I need some addvise

net min-home-x <= parport.0.pin-10-in-not

Arceye, I agree with both you and Todd.
I am no longer going to use Step Configuration for anything, if it isn't going to get Lcnc going in earnest I see no point in wasting anymore time with it. Thank you very much for the fresh hal and ini.
Talk about going above and beyond for a fellow enthusiast! I'm grateful.

I really thought I was helping the the situation with the wiring diagram, this is the way the machine was originally wired. I have another wiring diagram from the fellow who built the machine, it makes the one I sent look positively crystal clear, I have compared them carefully and they do match. 
This must be how the original “Indexer LPT” software (a windows based program) required it.

I intended to include the Z axis information for you, I got pulled away and by the time I returned to the email the thought was lost and I had submitted the post.  
Yes, Z is step/direction pins 2&3, and ampenable is pin 5. (A little late for that info now, I know).

Now, the good news.
I found I still had a limit problem after replacing the hal and ini.
Back when I moved the limit wires on the Z axis breakout as directed, I was concerned about an anomaly I thought I had seen there. 
At the time I was more interested in seeing if the drives and motors were OK than taking time to untie a possible limit switch knot. I set it aside for later, (now IS “later”).
I wanted to make sure I was not wasting your time so I investigated further. I',m glad I did.
I think the reason this machine was shelved was someone had screwing with the wiring for whatever reason and got themselves in over their head. Rather than trying to sort it out or pay someone to do that, the machine just got pushed aside. You would have to know the seller to appreciate this situation. Not a supprise!

I think I have this sorted out, your critique of these results should be interesting and helpful.

Lcnc is working, with just a few things that may or may not be problems, please let me know.

X axis: This one has a nice sound and travel with one issue, it can stall just as I hit an arrow key.
If I hit the key in the opposite direction it runs smooth, and when I switch directions back again it usually run
smooth in the original direction. An adjustment I hope?
It will home when I click the home button, all though it will hang there, I have to shut down the drive,  move it off the prox. switch by hand, and start everything over again to get my travel back.
The same is true of the max limit, when the prox. is tripped, it will not move anymore.

Y axis: In a word, sweet as can be, it will take a jog speed as high as it goes. (Not that it should be needed).
The limits react the same on Y as they do on the X axis. It homes and hangs, or trips max and hangs.

Z axis: (Before I start here, I have cleaned the drive box but have not disassembled the drive to check the connections as Todd suggested on the transformer to driver terminal as yet).
I have travel, it is gravely in sound, and it stalls sometimes while going down and often when going up.
I have the jog speed set at 4.5 in/min and the velocity at 62.6. These settings are best, with the lest amount of noise and stalling. I noticed page down moves it up, and up moves it down. where in the system should I fix this?
This axis will NOT home when I click the home button.
It will travel to max limit and hang as the others do. 

I understand the motion issues may be drive related, what should I do to confirm this? 

Thanks as always.