1) Why not run your wires straight from one side to the other? why did you put your wiring all along the edges?
It's far less work to connect the actuated tiers the way we did, especially with the maintenance shaft running down the center. It took only a few moments to wire everything together around the sides.
2) Possibly add a universal shut off (ie: a third wire running through all the actuators not connected to a timer) so you can actuate all the blocks for a final harvest before you go do other stuff
Well, for starters, wiring all 47 tiers with a third color of wire would take one person at least half an hour, and probably most of an hour. It's not worth the effort if you own a Rod of Discord, since you can just check the maintenance shaft. You could put a trapdoor below the maintenance shaft if you don't have a Rod. The farm also spawns only one plant at a time, every few minutes or so, so it's not a big deal to just log off (though I usually do check).
Depending on how high a Strange Plant spawns, it can take anywhere from a few seconds to almost five minutes to reach the bottom, so it IS possible to have multiple harvested Strange Plants in the farm.
3) Add a simple dart trap on every level (possibly connected to the shut off switch?) to harvest all the blinkroot that grows
I have half a chest full of Blinkroot, but that's actually a potentially good idea, for reasons I'll get into below. The traps will kill monsters too, though, and you generally don't want random monster loot, seeds, and plants to accumulate in the world or in your inventory. If you do that, you should probably trash the unwanted loot every so often and make sure you have one of each color of Strange Plant already in your inventory so that you don't lose any.
4) Since dye and strange plant checks are now done independantly why not add a couple layers of jungle grass for bait collection
This probably isn't a good idea, unfortunately. While they won't entirely prevent strange plants from spawning, what they will do is use up blocks for long periods of time. Strange Plants will not spawn on a block if any type of grass, herb, or dye plant is already there. The more empty blocks you have, and the longer they're empty, the more often you'll get Strange Plant spawns.
Because of this, dart traps to remove Blinkroot would probably increase the farm's efficiency. However, only a handful of Blinkroot usually ends up growing, so it's not a big deal.