Some news on this epic mess...
I've been running round in circles a little but have made some small progress:
Received the PLX9050 from China, it took me some time to unwrap it when I eventually did it was clearly a pulled and cleaned part not a NOS one, some of the corner pins had lost about 1/3 of their width.
Ebay seller is "yyen4650" just in case you want to avoid him too.
Anyway not having anything better I took a couple of thermal images of the original running then replaced the PCI9050 (it's only TQFP-160). Results were exactly the same PCI card not found, PCI9050 temperature exact same.
No luck with the PLX monitor software either.
Not knowing if my replacement PCI9050 was actually any good I started looking for another source, while looking around I discovered that some dual RS-232 boards used the PCI9052, downloaded the datasheet to check compatibility. As far as I can tell they should be interchangeable, just the 9050 is long obsolete while the 9052 isn't.
Scrolling through the PCI9052 datasheet I came across this: "Notes: 2k-bit devices such as the FM93CS56, are not compatible. The PCI9052 does not support serial EEPROMs that do not support sequential reads (such as the FM93C46L)."
Oh, crap! That's precisely what I used a 93C46L... Bad!!!
One EEPROM replacement and programming later, the board was detected by windows and the Ultima.exe software able to run, which initialises the scope's front panel and brings up a window with the DSO traces and menus. Scope seems to be mainly working although it looks like a recalibration will be needed, I'll have to look into the cracked resistor network on CH2 too later.
Next problem is getting the integrated LCD display running again. I was hoping for a dead backlight inverter but there's no display at all neither on the LCD or on the slow acquisition PCI card's VGA output.
The integrated LCD is connected to 30 conductor FFC socket named SK2, the backlight is separate.
LCD is a 10", NEC_NL8060AC26-11, 3x6 bit parallel bus model. The video path seems to be analog to digital through an AD9884A, then through U19 (EPM7128SLC84) before the LCD.
The analog video goes through groups of AD8055 voltage feedback amplifiers, one group before the rear VGA output the other before the AD9884A.
The problem is I can't seem to find the origin of the analog video anywhere on the board, AD8055 inputs all lead to SK1 - 15 conductor FFC connector on the rear of the board so i'm assuming the VGA source is elsewhere...
The illustrations of the back of the scope on the user manual don't show any other VGA output than the one on the slow acquisition board, I have a separate VGA PCI board but that was likely dropped in by the previous owner.
There's a "Microsoft SMS Mirror Driver" in the display adapters, I'm not sure how that works having never met it before.
If another owner could confirm this it would be quite helpful. Then I'd have to try and discover the FFC pinout.