If I'm reading things correctly, have you checked whether the hard drive is set for master/slave?
I have the 54831M and spent nearly a year repairing it (and thanks to the help of many on here, got it to work along with upgrading to XP).
Mine had booting issues in the beginning and it resulted in a bad hard drive.
You're correct, the unit has x4 Agilent chips. If any one or more are bad, you can't calibrate the unit (it aborts calibration when it gets to that channel). The chips no longer exist unless you buy used ones from China on eBay - I had to replace two and got lucky because they seem to work.
The first obstacle is to get the unit booted. Get a known good hard drive, or USB, create a bootable drive, and load from it. At that point you'll know if the motherboard is good.
Keep in mind, you have a PC in front of you, not an oscilloscope. This was how I approached the initial issues with my scope. Afterwards, I then accepted that I had an oscilloscope when the computer booted.