If you're wanting a multi-boot system, I'd recommend going with a hot swap 5.25" drive bay instead of using a boot loader on startup, preferably one that can hold multiple drives and comes with power buttons for each drive (Icy Dock makes a variety of these). Just power on or off the drives you want to boot, that way you don't have to hassle with installation order or worry about one OS doing something under the hood to your other OS's partitioned drive. Once I went with this as a multi-boot solution, I'll never go back to doing it in software. If your motherboard only supports IDE, you can always use an IDE to SATA converter, though I've never tested a hot swap bay with one of those devices, so I can't speak to compatibility.
Also, if you're going balls out on a win 98 rig, not caring about period correctness and all that, the biggest factor to me worth considering is whether or not you will want to play DOS games with FM synth sound. If you do, then you will want an ISA slot, which will basically determine your hardware configuration for you. If not, then your choices are much more open. I've used a Yamaha PCI sound card in the past that did pretty good FM, but compatibility was spotty and it sounded a bit washed out and muffled. Good luck with your build!