How do I actually get this server functioning?

Brief history:
- Snow Leopard Server working fine.  MacPro, Mirrored Boot Drive (RAID 1).
- Initial install failed and left the server in a reboot/install failure cycle with no recovery possible (Lion Server has no official recovery disk - apart from some tricks that have been documented in some places apart from Apple Support - where I keep finding some help and then finding 404 errors a day later as the help is pulled - about pulling apart the Lion install package to try and create a boot disk).
- FYI the boot/recovery disk approach that was mentioned above did not work on my machine at all.
- After splitting my RAID mirror and converting all drives to regular drives and restoring my Snow Leopard Server install using the SL Server disk and Time Machine to something functioning I was able to install the Lion Server.
- The I rebuilt my RAID 1 mirror of the boot disk and things are now functioning.
Notes:
- The Server application doesn't seem to trust the old server's certificates and almost every service is blinking green/off as launchctl tries to launch services and then they fail.
- My purchased SSL certificate was not present in the server anywhere seeming to have disappeared into a black hole so NO web services were functioning.  This included Wiki, Push, Web, etc etc.  I had to re-issue the SSL cert using the new server and add it.  Things seem to now recognize my SSL certificate now.
Questions:
- Services are all trying to start and failing.  I am getting many many log entries about this. I am able to log in using my domain account so it seems that OD upgraded OK (maybe). But everything else is a mess. Any suggestions on where to start cleaning up the mess? (This is partially related to my next question).
- Where did DNS, Firewall, Software Update Server, OD configuration go to?  I run my own DNS server for my domain, have reasonably customized firewall rules to suit my server and services. The server app has no mention of these items. Am I left with command line tools for these again? This would be several steps backward from the prior server.

Thanks - really appreciate it.
I can go and get out my bind and server admin command line books as necessary too. But I will take a look through this and see if I can restore some normalcy
I _always_ get suckered by Apple's server OS into buying and installing it when it comes out - expecting that my configuration will migrate and work seamlessly 'it just works'.  But I am now starting to take the view that this is just too painful an experience.
There really is no easy upgrade for Apple's Server.  (I have run various Linux servers in the past and had seamless upgrade experiences with those - Red Hat, SUSE, Ubuntu to name three have just worked out of the box on day 1 in recent years).
But the server just seems the same quality between Tiger - Leopard - Snow Leopard. The pain and lost weekends trying to make this work are hugely frustrating.
Here I go again - probably for the last time.

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    - it WAS a hardware issue with the Mini
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    - non-retail customers ARE treated as second-class by support.
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