I had another go last night using a miniATX board, Gigabyte H110M-DS2, and three PCIe to PCI risers. Processor I used was already installed, an I3-6320, but I am sure any supported processor will work.
Unlike previous attempts, I used an original Agilent recovery image expanded to 60GB. This is based on XP SP2 and Infiniivision 3.70 from about 2003/2004. I've never been able to make the documented recovery process work, so to recover that image, I used an XP VMWare VM on another machine with the scope's disk connected to a PATA to USB adapter, and attached the disk to the VM as a physical device. From there I could access the .GHO image. Booting an ISO of my own copy of Ghost 9.0 from many years ago, again in a VM, I restored the .GHO to another SSD and made sure it would boot on the scope. At this point I made an Acronis True Image image of the SSD.
Backing up and restoring disk images with new hardware is about ten times faster than trying to do it on the scope with its original hardware, even in a VM.
A fiddly thing about using a newer mobo is that I found that the UEFI graphical BIOS setup and boot selection doesn't always work with the old CT65550 graphics board. I had to keep removing and reinserting the display board pair as appropriate and use the board's integrated graphics when I needed to boot off my USB drive. I could try setting various parameters in the UEFI BIOS but there are many options, and I chose to leave that for another time, and I've been down that rabbit hole already without much luck. I also wanted to see how far I could go with default CMOS settings.
All I needed to do to boot the restored image was to retrofit the Skylake SATA drivers from Win-raid
http://www.win-raid.com/t11f23-Modded-Intel-AHCI-and-RAID-Drivers-digitally-signed.html ("Universal 32bit Intel RST AHCI+RAID driver v11.2.0.1006 mod+signed by Fernando"). I used Acronis True Image 2016 Universal Restore to retrofit the AHCI drivers. There was no messing about with any ACPI settings that I've needed to do before.
You may find you can achieve the same thing by slipstreaming the Skylake AHCI drivers into an XP distribution using something like nLite, and doing a repair install, but this will take quite a bit more time.
After that, I loaded the various Agilent specific drivers from a CD I'd made up with the .infs etc (see OP).
I ran the postsysprep.bat batch file in the C:\PciFilter directory from a command prompt as Administrator with execute protection disabled, and allowed a reboot.
At this stage, the scope app works, as do ACPI power functions. There are about five motherboard drivers missing, most notably no USB, Ethernet or HD audio plus a couple of other bus related drivers. I'll deal with those later once the OS is upgraded.
One further note, the OS is somewhat unsurprisingly requesting activation now, for which I have three days' grace. Hopefully it will allow me to to upgrade to Vista first before needing to do that.
I recommend using a modern SATA attached DVD drive at this stage as I have found the one in the scope doesn't read all disks, such as DVD+R for example, one of those irritations of the dim and distant past!