The copy of the manual I have is not helpful in regards to cabling, there are no illustrations showing where the various connectors are located. By careful checking of the layout for every board, I was eventually able to determine what goes where and all appeared OK. I did adjust the routing, particularly around the CFC board as a lot of cables cross over each other and I found at least 1 cable was fully snapped into place; that was obviously the problem as it's all working now and appears to be accurate based upon my signal source; I have a higher frequency generator which I'll also try as the one I'm currently using maxs out at 30MHz.
Now I can use it to repair my HP spectrum analyser!