First time boss down: 6 DKP
There is no mechanism to determine if it's a "first time kill." You'll just have to amnually set it when you do it.
Final boss for the instance downed: 8 DKP
Just make Nefarion, Ragnaros, Ossirian, etc, worth 8 points in the "Destinations"
Being there on time: 2 DKP
Make a Destination called "Molten Core - On Time" and make sure to associate the snapshots to the appropriate part.
On waiting list .50 DKP , Getting in the raid while in the waiting list is another .50 DKP
You can do this through adjustments or by manually overriding the value they receive (by putting something into the box next to the checkbox of their name on the "Raid Attendance" screen or the "GRSS Upload" screen).
Being there the whole time in the raid: 3 DKP
This is the one thing you mentioned that I plan on implementing a manual mechanism for. At the moment, however, you'll just have to manaully record this in the "Raid Attendance" section.
Killing a boss for second time or more is only 4 DKP
Make the bosses worth 4dkp by default in the Destinations.
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It's all in the reflexes.