Basics:
In a dual/multi-boot set up the installed M$ OS's install their boot/start-up files into the active Primary/system partition. The system files (the actual OS) go wherever you point them - even to another physical HD.
You removed the '98-HD and installed W2K on its own HD. When you re-install the '98 HD as Master or Slave you can only boot to/from whichever HD is Master? This is because the active Primary/system partition on whichever HD is Master has no boot/start-up files for the 'other' OS.
Your solutions:
1)
Install a third-party/add-in boot-manager (PM6x - can handle W2K - or one of the freebies out there...). You can then use this to select which Primary (and thus which OS) to boot to/from.
Using an add-in boot-manager will allow you use/see one Primary partition only; the inactive/unused Primary is hidden. In this scenario, to share data between the two Primaries (OS's) means you need an Extended partition on one of the HD's; Extended partitions are visible to whichever Primary is active. The Extended data area also needs to be a common file format; for W2K/'98 this can be FAT32 (even FAT16...).
2)
Connect the W2K-HD as Slave to the 98-HD; re-install W2K to its HD - in effect run set-up from a CD boot (or the 4 floppies), choose Repair and it will write a set of W2K boot/start-up files to the '98 system (active Primary) partition - thus establishing the basic dual/multi-boot requirement. W2K will add '98 to the W2K boot-menu and give you the dual-boot option. (Do not run the set-up/Repair routine from within an installed OS.)
Caveat: if the '98 HD is 'noticeably' slower than the new W2K-HD then you will not benefit from the W2K-HD superior performance/speed of access... The maximum speed of access to both HD's is determined by the speed of the Master HD...
Equally you could install '98 as Slave to W2K-HD (Master) and re-install '98 (in effect an overwrite...) and thus establish its boot/start-up files into the W2K system partition. Again you fulfill the basic requirement for a dual/multi-boot. This order of HD's means that if W2K-HD is 'faster' then it will still be able to perform to its best, with the '98-HD as its slave.
As you are understandably concerned about your '98 HD (its data) I'm inclined to favour any 'minor' sacrifice of performance of W2K-HD in order to retain '98-HD as Master to W2K-HD Slave (although setting '98-HD as Slave to W2K-HD Master should be OK...). Adding the W2K boot-files to the '98 system partition will/should 'not' affect the performance/reliability etc. of the '98 installation.
Otherwise maybe the boot-manager add-in util is the way to go?
http://www.xosl.org;
http://www.osloader.com
are both freebie boot-loader sources.