1 - how do you have a 'bot' that is permanently in a specified channel as an OP and will make automatically make specific users OP when they join the channel
Run one. Running bots is beyond the scope of this forum.
2 - how do you 'register' usernames with passwords???
You will need to run a services package for nickname registration.
3 - is there any way to remove the message UIRCD displays when connecting:
Your host is IRC.DOMAIN.COM [HOSTNAME], running UltimateIRCd(ArcticTiger)-2.8(07)
This Server was last (re)started on Mon Sep 10 2003 at 12:29:22 CDT and is located LOCATION --- etc
Its possible to do anything by modifying the source code.
Those messages are IRC Protocol messages however which MUST be sent out or bad things(tm) can and will happen. Connecting IRC clients use these protocol messages for several things. Some clients might have more trouble than others.