So an update. I've moved the 'good' ROM socket from my IIsi to the SE/30 logic board. I also decided to reflow all the solder joints on the PSU, analog board and CRT neck board. (I was having some picture stability issues even after a recap of the analog board, so thought it would be wise.
In my haste to reassemble the machine I forgot to connect the flyback anode cap to the CRT and unfortunately when I powered it on it shorted out to ground against the metal cage in the photo and one side of the suction cup melted. I disconnected power as soon as I smelled the burning.
I reconnected the anode cap and powered back on, expecting the worst, but the machine seems fully operational with a good picture.
Have I been lucky? Can I just replace the suction cup from a donor CRT and get on with it? And presumably it's safe to run it with a slightly melted cup?