The PSU on the JP6 is a "discreet" linear design with no 3 terminal regulators used. IC1 (UPC3423C) is an overvoltage detection IC that is connected to SCR1. This combination is configure to act as a "crowbar" effectively killing the 5v output if there is a regulation malfunction. This is used on the Digital 5v supply but not on the analog 5v (pin 3 of the PSU board). Is this voltage correct?
You say that with no load the D5v on pins 1 and 2 of the PSU board is good but it drops to 0.7v when the
JP's boards are plugged in. This indicates a couple of scenarios, it could be that IC1 on the PSU is malfunctioning or that the caps associated with D5v are "boarderline" (looking more like resistors in circuit than caps) or there is a fault on one of the boards attached to D5v (usually a capacitor across the power line on one of the boards).
Test the PSU by connecting a high wattage (couple of watts - a small 5 - 12v lamp will do well) load on the D5v output and look at the voltage across it and see what it does. If it stays at 5v with this load you can say the PSU is good. Next connect the other boards one at a time to the PSU, checking D5v each time till you
find the board that causes the PSU to shut down. Fault find the offending board, repair and you should be back in business.
You mention that SCR1 was removed from the PSU before you got to look at it. I'd say someone has had problems before and removed the PSU protection to get it working without actually rectifying the cause of the fault. This sometimes can work (in the short term) but WILL cause major problems further down the track.