A couple of general pointers:
In that era, the most popular motherboard chipset was Intel's i440BX. Your motherboard uses the competing (and popular) ViA Apollo which, while competitive, had some issues and quirks. With ViA based boards you would have to be more careful with BIOS settings, driver selection, etc. to get the optimal outcome.
#1 head-ache (after your BIOS settings are optimal) is the ViA 4-in-1 motherboard chipset driver package. Before you install any other drivers on Win95/98, you have to install this. Apparently the best version is 4.35 (4in1435v.zip) Why v. 4.35? See here.
#2 nVidia driver packages were fairly reliably optimized for the newer hardware and seemed to degrade in performance for older cards with every successive release. I remember when I got my hands on a TNT2 back in the day, and to try it out simply installed whatever driver was included on a cd-rom that came with a computer magazine I was subscribed to at the time. After the initial trial, I decided to do a clean install and download the latest drivers for an optimal setup. To my shock, after the reinstall games ran noticeably worse. I eventually traced the problem back to the video driver. It turns out the "outdated driver" from the CD-ROM was a much better fit for a TNT2 and Win98. That driver was Detonator 3.68. On AGP-based systems, I usually default to that one for TNT2s still, with DirectX 7.
#3 Your TNT2 M64 is a neutered TNT2. The performance is roughly on par with a first-gen TNT, so don't expect miracles out of it.
#4 Even early Pentium 4s are over 1 GHz in clock speed. Despite the Pentium 4 being less efficient per-clock than a Pentium 3, that is still at least a 2x speed differential between the platforms, not to mention your Pentium 4 probably ran on an Intel-chipset instead of ViA.
I wouldn't know where to start with on guiding you, but you should probably start from the BIOS (go over each setting and its meaning to make sure you're actually set up for best performance), then make sure you have the right expansion cards in the right slots on your motherboard. Only after that, would I do a perfectly clean install of Win98SE (no unofficial service packs), followed by the 4-in-1 drivers and then the video card, sound card, etc. drivers.