I promised to update, just in case someone has the same issue.
Swapping out the PSU solved the HDD problems.
So I didn’t have to find answers to Qs 1 and 2, but I can answer 3.
Once I had correct power supply in place, in fact before putting any other data drives in, I made a clone of the samples/VST drive (which I had indexed as “I”). I formatted an SSD which called itself “D” then ran cloning software. Once clone had completed, I put the new SSD in the same SATA position as the old HDD and renamed it “I”. Then I rebooted again adding my other drives and now Cubase sees it as the samples/VST drive. Job done.