Does the PEQ DB not have the notes field in the rules table? The notes fields help a lot and should have answered most of your questions here.
The regen percent is a percentage regen every tick. So, if you want people to gain back 2% of their total health per tick (no matter how many HPs they have), you would set the percentage rule to 2. By setting this rule, you can determine the max amount of time people will need to reset for.
Yes, the time field is in seconds, not milliseconds.
I really don't quite understand all of the experience setting rules, but I would suggest trying it as-is and adjusting as needed.
I am sure some are missing from here now, but here was the original addition of the notes field that I think should make your table a bit easier to understand:
http://code.google.com/p/projecteqem...lues_notes.sql
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