W2k has greater, more specific hardware needs. Items MUST be on the HCL. Past that, you will find it to be more stable.
As to the domain issues, W2K to W2K login uses Kerberos, which you'll have to decide on yourself. If you simply leave and rejoin the domain, the two W2K boxes will negotiate for you.
I'd move the PDC to W2K in a mixed AD mode...this would allow the W2KPro boxes to use Kerberos, and the W9X boxes would continue with the NT4 scheme, and all are happy.
If you move to a pureAD W2K domain, you'll need to install the AD aware Client Services for W9X (on the W2K Svr CD).
YMMV.