You seem to be making heavy weather of this - and looking at it as one big wiring problem.
It is, in fact several little wiring problems, each one fairly simple.
I have re wired my set up to a PC case for more room
I am not sure what this means. With Mach 3 there are three basic ways to connect to your P.C. All work, and it depends on your own needs.
1. I have a lead from the computer LPT1 (printer) port to a dumb (no power unit) Break Out Board in my control box.
2. If there are not enough inputs/outputs from your LPT1 port, you might get a commercial port connected to your computer which gives you additional inputs and outputs. This may or may not come with a break out board.
3. You can invest in one of the new smooth steppers, which connect to the P.C. via a USB port (These are new - so I have no idea what USB connection you are referring to, unless it is part of the C10)
I will assume therefore that you have a computer, and have connected it to your C10 breakout board via the printer port cable.
You require a 5 volt supply to the C10 board, which connects to the board on the top right hand side (assuming the printer port cable at the top)
I do not reccomend that you take the 5 volt from your P.C.
At the same time as connecting the 5 volt supply, connect a 5 volt jumper to the enable pin - next to 5v - or you will not get any output from the board.
The paperwork that comes with the C10 is misleading. You cannot get inputs and outputs from all pins, if you are using the computer LPT1 port. If you are using the LPT1 port you are limited to 3 sets of pins - and they cannot be altered for input or output.
Pins 2-9 are outputs only - normally used for connecting to the axis drives (in your case the Geckos)
Pins 1,14,16 and 17 are also outputs only - I use mine to control Spindle motor M3 M4 and M5, together with coolant
Pins 10,11,12,13 and 15 are Inputs to the system - only these 5.
The rest of the wires - 18 to 25 are signal return wires to the computer.
This completes your C10 board. If you connect this to your computer and power up the 5 volt supply, you can test the various pins. My favourite way to do this is (on Config/Ports and Pins/Outputs) allocate M3 and M4 in turn on each pair on pins. By typing in M3 or M4 on the MD! line of Mach 3 you can see the pins change voltage with a voltmeter.
Your Geckos are completely seperate to the BOB and should be treated as such. They should be wired with your supply voltage for the drives and firmly wired to your motors, as per their own diagram. When you turn on their power supply, I think the red led will go on ( I might be wrong on that)
To connect the BOB to the Geckos requires three wires to each drive. These should be taken from the bottom row of pins - 2,common,3 - 4,common,5 - 6,common,7. the numbered pins go to the step and dir on the Gecko, and the common goes to the Gecko common (which is next to the step and dir pins.) The common should be +5 volts, so ensure that the jumpers for pins 2 - 9 common (above pins 4 and 5) are set for 5 volts. The Geckos have a disable pin - leave this unconnected.
This should get you going. Only do one drive at once, do not try and do all three together.
I assume you can then work through Mach and set up the various configurations - if not, come back and we'll have another go.