If your primary interest/concern is with late 80s to early 90s DOS games, you either want a 386 or a 486. If you go for a 486, it can be effectively slowed down using options I describe at the end of this message.
DOS 6.22 is OK, and can be found easily.
I'm not an expert on ISA or VLB VGA cards. Over the years, I've briefly tested about 30 of them, and none of them provide as good a signal quality as a good PCI video card, if that's an area of concern although it may not be. For PCI, leileilol's suggestion of a S3 Trio 64v+ 2MB is a good one, because it has good compatibility. I like cards manufactured by STB, and they do a S3 Trio 64v+.
SB Pro 2.0 is OK, and also kind of era appropriate for your needs. For your area of interest (80s-90s), you could get an MT-32 or a CM-32L or another variant. There's a small number of games which need a specific version to sound correct. The SCC-1/MIDI will not be era appropriate for your needs, although the old SCC-1 card sounds incredibly good, when listening to games using MIDI music. (Games supporting MIDI began circa '92+.)
As sliderider pointed out, old mobos are getting expensive and thin on the ground. I would grab anything you can for now, and just see how you get on with it. If you have a choice, I like UMC chipset-based PCI 486 boards because you have these flexible bus speed options: 20,25,33,40,50,60,66. The first 4 speeds are useful for slowdown projects, as mentioned at the end of this thread.
Also, the old stuff you need for a 486 system are only the mobo + CPU + RAM + video card + sound card. 486 CPUs aren't rare, neither are 72-pin SIMMs, although some of the older mobos only accept 30-pin SIMMs. Era appropriate video cards aren't rare either. It shouldn't take you long to get a SB Pro 2.0, eg model CT1600. Everything else can be new. That's the ATX PSU, ATX to AT PSU adapter, 5-pin to PS/2 keyboard adapter, PS/2 keyboard, all cabling, 3.5" floppy drive, HDD/CF, and optical drive. I'm not sure which new cases can accept an old 486 mobo. You can buy serial mice fairly easily. Some 486s have PS/2 ports, but not many.
I would recommend a 486 SX-33 CPU. The reason for this can be found at the end of this message.
For a 386 system, just fill up the SIMM bank with whatever it needs. 4MB will do. For an early DOS 486 machine, 4MB will also be OK.
I would recommend an NEC CDR-273 quad speed CD-ROM drive. They are quiet.
Re: 5.25" and 3.5" Floppys. Yes why not.
I would put Windows 9x on a slot 1 Pentium 3 machine. Around the 1GHz speed will cover almost all ground. If you're lucky and you can get a Powerleap adapter, then that can go up to about 1.4-1.5 GHz. A good mobo choice is Asus P2B, but there are lots of others available.
PS. How to slow a 486 down. Please see this thread here. Scroll half way down, and look at the large table. It's a 3DBench benchmarking results table, using a 486 SX-33 CPU. All I do is adjust the mobo's resources, and I get a *very granular* 3DBench results table. And those tests are far from complete. The point is, you can slow a 486 down to achieve a variety of speeds for 286 and 386 games. Other systems won't be as flexible as this, even a 386 itself!
