First off, sampling hardware sample-based synths is illegal. Most soundfonts are illegal for this reason actually: all of these sounds had to come from somewhere, and 99.9% of the time they're recordings of hardware MIDI modules or early VSTs.
What you want to do are MIDI covers of these PC-98 tracks, it's not really remastering at all. Keeping things simple, remastering is simply making a new master of an existing mix, usually for the purpose of taking advantage of modern storage media/formats. For example, Digital audio (CD, mp3, wav, etc) can be made considerably louder than vinyl, so when 80s albums are re-released they're also remastered, mainly to make them sound louder. The source audio used to create the CD master is the same audio that was used to create the vinyl master. If anything is re-recorded (guitars, drums, etc) it's not really a remaster anymore.
Now, even if it was legal to make a SD-90 soundfont, it wouldn't really sound like the real thing. It's hard to explain to someone who's not hardware savvy, but these synths do more than just play sounds stored in ROM, there's actually lots of dynamic variables that affect the way the instruments sound. For example, the SD-90 has a characterful filter that changes shape based on the note velocity, note played, the order the notes are played in, whether more than one note is being played at a time, and a bunch of other things. Many presets also have varying degrees of constant pitch instability. When sampled and made into a soundfont, the instruments lose all these dynamic variables making them sound dull and lifeless. The same goes to... almost every soundfont, not only for the reasons stated above but also because the person doing the sampling needs to understand how the synthesizer works for the stolen sound to even sound decent. Don't expect people who do things so obviously illegal to be very bright.
It's also important to remember that there's more to the ZUN sound than just the SD-90. You need Cubase Pro and his VSTs too, so if you can't even afford the SD-90 it's better to not even dream about making ZUN-style music, specially if you aren't able to make your own music and arranges already.
BTW the SD-40 doesn't exist.
While the older Windows games (6 through 9) tend to use MIDI-esque sounds, even in the prerendered .WAV soundtrack, the newer games' soundtracks aren't necessarily a MIDI-to-wave conversion. I suspect samples from a synth, but with heavy effects added on to make the music sound the way it does.
There's no such a thing as a "MIDI-esque" sound, because MIDI just tells synths what to do. There's no sound you can associate it to. ZUN has been using the same main synth since Kioh Gyoku, and the same set of VSTs from IN to UFO. The differences in sound come mostly from him figuring out how to use his stuff.
You'd probably have better luck using the Roland SC55 wannabe sound set included with Windows and lots of free time tweaking various postprocessing effects to get the sound you want.
In short: you can probably make your remixes sound like TH6-9 easily, but doing them in the style of later games would be much harder.
I don't even know if this is a serious suggestion.
