It seems the DMT was still wet when it was weighed. All the DMT combined was weighed again and only 800 mg, so 0.8% yield. Perhaps a 3rd toluene pull should have been done on the basic soup (which I still have). Or more likely the volume of ammonia washes was way too big and a lot of DMT dissolved in them. With the final wash it seemed like the DMT was dissappearing before my eyes! (or maybe it was sodium carbonate like downwardsfromzero suggested)
There are still things I don't understand. At pH 11 (first mini A/B re-base), 99.5% of DMT should be in freebase form. Then why did pH 14 (second mini A/B re-base) crash out so much more DMT (volume of water was the same: 400 mL) ?
A/B seems to have its proponents on this forum. My hope with A/B is a less muddy basic soup and quicker emulsion separation after shaking. Also, smaller volumes (basic soup fit barely in 1 liter erlenmeyer, largest one I got that has a PTFE stopper) and much less NaOH needed. According to one user, the acid soaks can be done rapidly by siphoning rather than filtration, and reducing can be done directly on a stove on high heat without reported losses.