You've mentioned in your original post above that you formatted your HDD to NTFS and you are trying to install Win98 - is that right? If so, then that will not work because any Win9.x based OS will not suport NTFS. Therefore you need to format your HDD back to FAT32.
In my opinion, you are really going backwards going back to Win98. I understand your printer/scanner won't work under W2K but trust me - if you're budget allows for a different printer - buy it. Cuz Win 2000 Pro and XP is rock solid. A better option is to do a dual-boot on your system if your HDD is large enough to take both OSes.
Now back to your jumper issues.
I replied to your PM about jumper settings and that link i gave you should further clarify the issue. What i am confused by is this:
Originally posted by wam:
Used old hard drive with win95 and the system ran OK. Tried to add WD hard drive as slave BIOS won't recognise it.
So you have one HDD w/ Win95 and another HDD that has been formatted with NTFS. Am i right? I guess i don't understand what you mean when you ask me if you should reformat? You've already done the 2nd one. If you are wondering if you should format the Win95 HDD then the answer is NO unless you are having serious crashes or windows problems. And so far, you've given no indication that is the problem here. You said it's booting up slowly. That could be that either your HDD spindle rate is slower than your previous one (thus attributing to the notice in slow speed) and also you should keep in mind that Win 2000 / XP boot up much faster than its predecessors
If you're BIOS sees both HDDs and sees them properly as master and slave, then you should be good 2 go. There's no more you need to do w/ the jumper settings. You said you were able to boot up fine after you set it to slave. The thing you need to decide is whether you want to do a dual-boot or solely use Win98 only. If you choose the latter, you need to format your HDD FAT32.