Here's an MS shooter for the floppy drive problem. Don't know how much help it will be, since you've already done some of it; but I'd follow the drill anyway. Maybe something in autoexec.bat or config.sys?
http://support.microsoft.com/default.aspx?scid=KB;en-us;q131690
(I'm not sure what kind of "pci" problems you are having, but you do have duplicate entries on IRQ9, I don't think that's usually a problem as I see it a lot, but it might be possible to get rid of them by removing both in Safe Mode and letting Windows redetect. You may need to reinstall the Via drivers after that.
You also have your Video card and Ethernet adapter on the same IRQ. I don't think that's the greatest idea; maybe you should try moving the Video card to where the Ethernet adapter used to be and see if you can get them separated.)
You could have some funky motherboard problems causing the whole mess; I don't know what else to tell you. Bad shutdowns can also sometimes cause a corruption of the cmos, but reloading should resolve it. Sometimes the shorting jumpers are a better way to purge things.
In any case the floppy issue really should be independent of the remarks in parenthesis. Since you did some cleaning, you definitely want to double check how well the floppy cable remains seated.