Quite honestly, I would just install a fresh 2k installation on your new drive with apps etc, transfer what you need from other 2 drives, then wipe them & use one as second (backup?) drive, if that's what you want.
Assuming you have an M$ 'standard' 98/2k dual boot, then yes the C: drive has boot.ini and more importantly the whole of the boot sector (2k's) which loads both operating systems. You could just create a boot sector on the new 160 GB disk (which would be first - C: drive in the machine) which would boot the 2k installation on D:. Just like this:-
Create a 2k boot floppy - copy boot.ini, ntldr, ntdetect.com to newly formatted floppy drive.
disconnect 98 drive and connect new 160G drive in its place - then boot machine using floppy - into 2k. use 2k's disk management to create/format an active partition on new drive (C

. Copy ntldr, ntdetect.com, boot.ini from floppy to root of new partition. Reboot into recovery console -
(you'll need administrator password - probably). From there run fixboot c:. Reboot without floppy - machine should boot 2k from on D: drive from new drive. You can then edit boot.ini to remove the 98 entry (usually C:\="Microsoft Windows"

. Remember 2k on D: may not boot if you mess with C: partition (but you've always got the floppy).
There are various other approaches you could take - but as I said at top, I'd just start fresh!