I'm going to have to disagree about there not being much to learn about a 386 system. If you're used to dealing with pnp systems then you'd probably have a hell of a time configuring a 386.
Getting a name brand unit is probably a good idea, because at least you'll be guaranteed some kind of quality. There are a lot of shitty 386 boards out there. Generally the best quality boards are made by big companies like Micronics, Intel, AMI. Many name brand 386 computers used boards from one of those companies. The only downside is that the BIOSes on these systems don't let you adjust much.
What you probably want from a 386 system is a 32-bit DX between 25 and 40MHz with some cache on the motherboard and an external battery. Dallas clock chips are usually trouble, and that's what PS/2s use. There is a work around available, but it's a pain in the ass.
Newer IDE drives can work on 386 IDE controllers without a problem. All you need is to get the drive overlay software that is usually on the drive manufacturers website. This will help you break past the 512mb limit of your 386 BIOS. However, keep in mind DOS is still limited to 2gb partitions, so you'll need to break up a large drive. I wouldn't mess with a new IDE controller, because they aren't always compatible with modern drives either, and I think they don't coexist well with overlays.
"Will the highways on the internets become more few?" -Gee Dubya
V'Ger XT|Upgraded AT|Ultimate 386|Super VL/EISA 486|SMP VL/EISA Pentium