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Reverse it all. Set them to "can store energy", or whatever the "not full" condition is. Send a red pipe signal, and invert it at the lamp - "red pipe signal off" = "redstone signal".
You can't safari net any boss-class mob. Hmmm, that makes me wonder... Quest Rams aren't bosses. I have some testing to do! (Off-topic for this thread, though, as TF ain't in MF2)
Hoppers are a little less ugly and more in keeping with the aesthetics of the construct. An import bus pointing up at the under-side wouldn't look too bad.
Or, Hungry Chest.
I have seen non-node trees convert, but it is unusual. Maybe that was a bug in an earlier version of Thaumcraft.
Those splash potion things can occur on any level of the crypt. I found them right by the stairs down from the entrance.
I agree, it's unlikely, but It's possible that each plant might have its own metadata on when it last grew, and the lamps might throttle themselves by not growing the same thing too quickly. I have no idea if that is the case.
Yes. Each lamp every so often reaches out to a random growable thing within its range and advances it on one growth step. Each lamp operates independently. I don't know whether the scaling is linear or not, two lamps might try to grow the same thing at the same time and only grow it one step...