Hi Stuart
Glad things are improving - of course without knowing exactly what's changed it's difficult to comment. It seems that you do indeed have a port/BOB problem on a couple of pins but let's leave that aside for the moment and concentrate on the fact that you have 4 motors running so obviously the other pins are good.
I have a few suggestions. Some I know to be correct, some I think are correct. I'd be grateful for comments where folks disagree.
You say you measured 3.5A. This doesn't sound right. Where exactly did you measure this? If you have each of your drivers set to limit current at 3A (which for your motors you should have) then I would expect the total current supplied from your PS to be around 8A at 24Vdc for the 4 motors.
Am I correct in thinking you appear to have a switched mode power supply? Mariss at Gecko used to recommend adding a capacitor at the output of a switched supply (like you automatically would have in an unregulated supply) but this advice seems to have been removed from their updated stepper guide so I'm not sure if this still holds but it makes sense to me at least.
From your pictures it looks as if you have a mixture of star wiring and daisychain wiring from your PS to your drivers. I'd suggest you make it all star wiring. Again see the excellent blurb on driving steppers on the gecko site.
I see your supply is actually 17A at 24V - wow that is some overkill - shame it wasn't 8.5A at 48V
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Just for clarification, don't worry about measuring current with or without mechanical load on your steppers - it makes no difference to a stepper.
Anyway - just a few thoughts.
Ian