I can't answer all of your questions, but...
c) Would you recommend an upgrade or rather a clean install of the Xymon server? - I'm not too concerned about losing the past months stats at this stage.
A clean install is always better. I find that test systems (mine, anyway) tend to get little bits of test code or test config left behind, an odd system gets forgotten about in the monitoring system or an old script doesn't get removed.
If you go for a fresh installation on the production server you are starting with a blank canvas. That plus all the knowledge you have learned from your test system means you will have a clean set up right from the word go.
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