Reinstalling windows without changing MBR

No, Windows 98 rewrites the Grob loader. The grib loader writes info to the MBR. Since I don't know what Linux you are using, look at the docs for Grub. My preference is you use a boot loader like Boot Magic as a part of Partition Magic. I used to have 10 OS's on my machine and I didn't use Grub. I pointed Boot Magic to the Linux partition ot load.

Have no experience with GRUB, but with LILO you would reinstall Windows, then edit LILO (should be able to boot into Linux using a boot disk) to reflect the configuration (would probably be the same configuration you are using now) and then run LILO to reinstall it and get yourself back to the situation you had working before the W98 reinstall. That would correct the MBR (which W98 would have overwritten when you reinstalled that OS) and make LILO the boot loader again. GRUB procedure is probably similar. (See the man file.)

I have not used BootMagic or the other one (Boot Commander or System Commander?) but have heard that they are good -- but why pay when you have such good free alternatives?

As to question 2, yes -- that is one of the beauties of the Linux loaders. See GRUB man file.

As to 3, I am not sure. Most installations I have heard about do it the other way, loading the Windows OSs using the Linux loader. I have had several systems dual booting W98 or NT and Linux (Red Hat & Debian) using LILO and it works great. Some people think LILO is difficult to configure but once you read the man page or consult a good Linux book you see that the procedure isn't that bad and it gives you total control. It is simple, reliable, and free -- what more could you want?

Good Luck!