The more worrying issue is that the new hard drive seems to have the same "clunk-whirrr" issue that the old one had - and four of the files that were downloaded as updates are giving i/o errors. This leads to two conclusions - first, that the i/o errors broke one of the updates, which in turn messed up some important system file somewhere, and second, that maybe the IDE controller on the motherboard is having issues, at least for that channel (the Windows drive is the only one on the first IDE controller, the Linux drive and DVD writer are on the other controller).
(and in reply to
As it happens, I have a spare motherboard, identical to the current one, so I could conceivably swap everything onto that, reinstall Windows again and see how things go. That's starting to sound like a lot of fiddling about, though ...