Small update to where I am at.
About the dead extruder.
Fixed: Due to frequent crashing of the RepRap host, the extruder goes way over temp, this eventually caused oxidation on the contacts, so I have cleaned it up, and made fresh connections again, and the hot end now works.
Reading on the forum someone mentioned about just hooking up the two lines from the motherboard that goes to the extruder board, instead just hook them onto the stepper driver 1.2 board that I have, and it works, what a relief that I don't have to fudge the silly Arduino code. I forgot that the enable line is automatically held in an "on" state.
The opto end stop and the steppers only driving in one direction problem.
Fixed: I am a douche, NopHead told me that the driver boards NEED the endstops, even in "dry" mode, so I made one endstop (opto), and the board its connected to goes both backwards and forwards, thanks to him that problem is solved.
The second opto endstop failed, I just couldn't get it to work, so instead I rummaged through my parts *ahem*junk*cough* bins and found a few tiny microswitches. I bent the lever so that there is no chance of the top of the lever biting into the plastic of the flatbed scanner, wired most of it up, just got to solder on the ethernet cable tomorrow, and th x axis will be ready to go backwards and forwards.
I felt that with the x axis flatbed scanner having the opto endstop on the moving carriage was going to be a bad idea anyway, just gave me the final nudge to use a microswitch, and have it glued down on one fixed end.
One thing has gone wrong, and i'm out of cash, quite literally, on one of my V2.3 driver boards the chip is blown, however I can get one or a few from the local BIG electronics supplier RS components, but as I said I have no spare cash, so the Z axis has no driver for it at the moment.
Thats not a really big deal right now, as my attetion is getting the extruder completed and running, so I can bolt it to the Z axis, and finish the mechanical part of the Z axis.
Next week, I suspect that Tim Carr from MindKits.co.nz will have finished his Mendel, so i'll be oogling over that at the Arduino next week Thursday.