Very interesting! I recently finished Deus Ex myself. Despite having several V1, V2, V3, and V5 Win9x machines at my disposal, I chose to play it under WinXP SP3 using the Deus Exe mod with these specs:
PC Chips M861G v1.6a motherboard
Athlon 64 3400+ Venice S754
1GB (2x512) RAM
NVIDIA GeForce 6 6800 GT
SB Audigy 2 ZS
On my LCD monitor at 75hz, max FSAA etc, I consistently got 75 FPS, except for when I first met with Helios. The poisonous green fog at the base of its "pedestal" caused dips into the 30s.
I was trying to compromise between keeping the game original vs getting maximum performance with some 3rd-party bug fixes. At one point, I did try running it in GLIDE mode but I couldn't tolerate the jaggies. Back in the day, jaggies didn't bother me. 20 years later and they really bother my eyes. So, 6800 GT it was with FSAA maxed out.
Some games are still OK without FSAA. Others, such as Deus Ex, benefit greatly from it.
By the way, there shouldn't be a difference between 2.5" and 3.5" SATA drives. If you're having problems with 2.5" drives, you'll probably have similar problems with 3.5" drives. Make sure you're using drives with 512B sectors. Most modern drives use 4K sectors and may cause problems. Try partitioning them using the original DOS FDISK included with Win9x. When it comes time to choose a size, use a percentage rather than a whole number. For example, on a 250GB drive, choose "25%" for a 62.5GB partition. Then wait... and wait... and wait...
A few years back, I wrote a Win98SE setup guide and posted it here:
Generic Win98SE Installation & Setup Guide