Does DMT-Acetate become Polar in H2O, with added NaCl?
Does NaCl cause DMT acetate (or any acetate) to become polar in $\ce{H2O}$? 


In aqueous acidic solution, that is in the presence of a sufficient amount of acetic acid, N,N-dimethyltryptamine is protonated. The acetate is the counter ion of the ammonium salt. The compound does not become more polar by adding sodium chloride!


  Will the DMT acetate have migrated into any of these two polar layers?


Are you having two polar layers? I doubt it. You're having a top unpolar layer, the aqueous layer and some gunk.

Take the separated aqueous layer, neutralize carefully, extract with an unpolar solvent of your choice, dry over sodium sulfate, remove the solvent in vacuum. If necessary, recrystallize and determine the yield.

Please keep in mind that DMT is a controlled substance in many countries!