Sounds like a heck of a project.
The LEDs are duel / bi colored LED packages hence the 4 legs.
Pins 3 & 4 go to a 150 ohm pull up to Vcc.
LED's Pins 1 is the fault LED via an inverter (U3 & U5) and the back plane EPM7064 power driver controller (which likely is not working in your project).
LED's pin 2 in the activitive LED which runs directly to Pin 77 in the SCSI connector for each slot.
Hope this helps.
I completed the project and have detailed it on my blog, here: http://vvenesect.wordpress.com/2011/08/12/converting-a-servers-scsi-backplane-to-use-sata-drives/ . I hope others here will find it useful!