How long can the lye and solution sit for? Leaving the solution sit for 48 hours before extracting with naphtha. Hopefully this wont have any negative effects on batch potency. Any experience or knowledge of?

As far as I know the NaOH solution cannot react with the alkaloids we're trying to extract here and especially not so if you don't heat it up to much. Room temperature should be fine (wasn't saying you need to cool it either), all that happens in this stage is that NaOH, the stronger base, is displacing N,N-DMT from it's place in a salt. Therefore the DMT is in form of a freebase and the sodium salt of the DMT salt is formed.

respect

It can sit for weeks and still be fine.

Mine sits for days on end all the time... seems fine.