For a dual-boot '9x/NT the c: system (active primary) partition 'must' be FAT16... which is probably what you had with '95/NT.
In a dual-boot '9x/NT environment, NT deposits its system (start-up) files into the C: system (active primary) partition... and this 'must' be/remain FAT16... Having installed '98, presumably into the C: primary partition on your first/master HD, as FAT32, NT can't see it... (NT can't 'see' FAT32...). Installing '98 and making the C: primary partition FAT32 has, in this case, effectively/overwritten hidden the NT boot-loader. If the C: primary (system) partition was FAT16, then all you would have to do is run the NT ERD sequence and you would be able to recover/re-access the NT boot-loader/boot-menu, and you would have your dual boot... Normally '98 is regarded as NT friendly and doesn't 'normally' overwrite/affect the NT boot-loader... (as long as it isn't installed FAT32 into the active primary partition).
You have options, which include, amongst others, converting the C: partition back to FAT16 (use PM, currently version 5).
Visit the link below, which is one posted recently re this whole 9x/NT issue...
http://www.computing.net/windowsnt/wwwboard/forum/4558.html
If you are willing... consider using a Boot Manager and this will enable both HD's/OS's... then visit:
http://www.webdev.net/orca/default.htm
which will offer assorted options in this vein...
Personally, I'd start afresh with a new '98 installation, and follow the info given on the first link posted here... Your NT is 'safe' on your second HD; you just have to re-arrange/reconfigure things on the first HD...; and then run the ERD again at the finish...
Good luck,
LM-S