Game crashed when I went to remove my Shadow Embellished Warpwood Wand from Tainted Magic equipped with a Time focus from the same wand. Upon reloading into the world, the wand was missing. http://pastebin.com/csFjrxXf

Have you tried the same actions with wands from vanilla Thaumcraft or other add-ons, with and without Foci?

I just had a crash while moving an amber wand with thaumium caps to the wand slot on the terminal. On reload my wand was gone. However, I was moving the wand without shift-clicking and I don't think I actually got the wand to the spot.
FTB Infinity Expert mode:
crash-2016-03-28_18.30.07-client.txt

#274