Maybe you're having the majority of your problems with the 98 box?
NT4 Definitely did NOT support Active Directory.
Microsoft does have an "Active Directory Client for Win9x"
Try searching for that and installing it on that 98 machine....but I must say that given your scenario....you're better off starting from scratch with a new domain name. I know it's a lot of work and reconfiguration but at least you'll know it was done right. If you can't rename the domain because of hosting issues or whatever....I would plug your old server back in and read those articles mentioned above in great detail.