Deconstruction tables suck because they can't be automated. You need to click on them to get the aspect. Inversely, whisperweed is so good it's practically a cheat. 1-5 aspects every 15 seconds or something and you just have to be in the general area. I set them up around my main crafting area and I never have to worry about aspects. The warp is actually good because it's all temporary but counts towards the eldritch revelation. You can soap it away.
If you haven't done it already, you should set up some endoflames to consume coal or charcoal from an automated farm and then take that mana and feed it not only to your Whisperweed, but an Euclidaisy as well. The later seems to generate an ethereal essence every 10-15 seconds or so. I have five set up near my thaumitorium with a golem chucking them into the furnace (I think if you slap an entropy upgrade in them, they'll ignore NTB data so you can direct him to just pick up essences). I basically always have a full stock of essentia unless i am doing some heavy infusions - with all left over going to an essentia crystalizer and then to an array of storage drawers. I checked it out today and I had over 6,000 crystalized auram
When you factor in the livingwood wand, Forbidden Magic's Botania items really makes getting started on Thaumcraft super easy. Maybe too easy. I kind of think the same thing about Arcane Arteries and Blood Magic. It makes getting started on Blood Magic trivial. You can have a tier 3 altar set up in under an hour.
I definitely remember that some rare instances of warp from the whisperweed was permanent. Might be rare, but it happened to me at least once or twice. I just reached a point at which I need no research points anyay though. I finished every research that is not gated by the primordial pearl. At least to my knowledge, could be that Automagy has some more surprises left in store for me, since it seems to do a lot more with gating it's progression behind scanning what it offers. I had a setup of 9 endoflames which I fed coal blocks every now and then, but recently I ripped apart my base, dug up a 6*6 chunk area for a proper base and just started cleaning up the several working places.
My farm is now 4 chunks large with 4*4 patches for most plants, some get more ... like netherwart (excellent source for praecantatio thanks to forbidden magic.
My witchery area is another 4 chunk large platform with dirt on it, on which I experimented with the different Botania pasture seeds for some neat varying grass colours. The altar has a bit more than 12k power already, now I just need to full the chalice and make a pentacle. (I had a setup consisting of 3 enslaved Hobgoblins, 2 or 3 golems, an infernal furnace and 2 magic mirrors which was effectively an infinite koboldite farm ... and, by accident, a neat passive experience farm. (Though the brain in a jar caps out at enough EXP to get a bit over level 40 up from 0)
I am also hoping to get AE2 going so that I can get rid of my mess of chests. It got so bad that I managed to lose a white bag ... I have 6 binnie core compartments and 7 enhanced inventory chests ... I have a vague system of what I put where, but it's still a huge mess.
... but before I get stuck trying to describe everything via text ... I just threw together a quick album showing off my base.
http://imgur.com/a/4cjZt
The only thing I haven't mentioned is that I will likely dig away a 9*9*9 area for some mariculture fishing. Breeding in general is something I didn't do much off. Just watched some modest queens&drones make parched combs and bred maybe 2 or 3 generations of fish.