I went into the system hotkeys as you described, they were all set to 999 numbers on all them.  That fixes that part.  Thanks.  However, now it seems that my axis only travel on part of the available table shown on the display.  Even though the direction arrows are proper now.  Could that be my soft limits?  my available cutting area I have 48" of gear rack on both axis except of course my Z axis which is probly around 6-7"inches. actually just free jogging it looks like it thinks theres still a phantom table next to mine, and I can only jog around about a quarter of the dotted line that represents my available table size.  Any suggestions on that?

It is indeed the soft limits that define the size of the table view.
Hood

hmm, I have them set at 100 for soft max and min max except for my Z axis of course. Which is the way they were set from installation. I wonder if there is a bug or something because now I loaded a .tap file of a simple bracket 3x3' in size and cant even see a view of it in the program run table display.

That will make Mach think the table is 200 long and thus you will overrun the table and soft limits will be pointless.

When you Home make sure Machine coords are being set zero (option in Homing and limits) you can check this by looking at machine coords by pressing the button.
Set X and Y min to 0 and X and Y Max to the distance of travel on each axis. Z is slightly different, Z Max is Zero and Z Min is the amount of travel but as a negative number.

Hood

I did a search on my new Z axis problem and found a post you commented on Hood. 

your post
"Ok if you move lower left lower corner and Z fully up and then press RefAll button the Machine coords should zero. That is the only way you can zero the machine coords, well it can be done in VB but .... Anyway if the machine coords do not zero then you may have one or two things wrong, both are on Homing and Limits page (from Config menu) Make sure you have the Auto Zero option chosen and secondly make sure you do not have a value set in Home Off box.
Then for your soft limits you want X and Y Min and Z Max set as 0 and X and Y Max and Z Min set to their respective axis travels, Z being a negative value.
You should then be able to jog to lower left corner and when you press RefAll the machine coords will zero and you should now be able to use Soft Limits."    end of your post.

My problem is almost the same as in this guys post.  When I hit ref all to get rid of the red outline on the axis boxes and make them green thus getting a successful machine coordinate setup, My Z axis just keeps going and is still going.  I decided to take the pinion gear off because it chatters and will probably destroy my axis, to see if it ever stops but its still spinning as I'm typing for at least three minutes now seemingly to no end.  I have my homing and limits set up just as you described.  There is no value in Home off box, and  auto zero is checked.  Both X and Y axis will go to home as there instructed to lower left, but the Z axis will just keep on going.  Z axis is set at soft max 0.00 and soft min set to -8.00 even though i have about 9 inches of travel on the Z axis. As you can see my soft limit setup, check out the DRO on the Z axis its at 1,687 and still going. 

Not really following regarding the "Z axis just keeps going and is still going. "

Do you have home switches on your machine?
Hood

I have one home switch that is used on my z axis to refrence the top of my material, on a floating plate, from no sleep studios.  The z axis will come down, reference the top of my material, travel upward, and will continue traveling upward + and will not stop.  It continues to travel in a positive direction. It will hit the end of travel and still try to continue in a positive direction, and does not stop until i manually stop everything.

Ok so it sounds like there must be a macro to do this reference, in the xml attached you do not have any home/limit switches set up so with the standard code in the RefAll button all that should happen when you press the RefAll button is Mach sets the machine coords at whatever position you are at.
 No axis should move when pressing the RefAll button if you do not have any home switches set up in Mach. If your Z is moving when you press RefAll then the script in your RefAll button must be customised and thus I would need to see it to see what it is doing.
The other option may be that the xml you attached is not the one you are using.

Hood

http://youtu.be/sq_nNsaRXIQ
Hopefully you can view this.  Give you a little idea on whats going on.  For whatever reason its doing this on the downstroke now when it comes down to reference material.  I gave up on that xml file i posted and started fresh.  So i do have my  only home switch operational verified in the diagnostic screen of mach3.  When i press switch it lights up on the screen.

I can not see what you are doing in that video clearly

What are you pressing to make the Z move down to the top of that box or whatever it is?

Hood