I always got around 6% yield in freebase which is on the higher end of what is reported from rue extractions. and yes longer boils will ensure all harmala alkaloids are extracted. you can always keep the seeds and do more boils later. pressing the liquid out of the seeds between boils is maybe not necessary but it reduces the number of boils needed.

freeze precip? i haven't heard of that for harmala extraction. but yeah resting the tea in the fridge for a day and then discarding the stuff that settles at the bottom makes the filtering easier and results in cleaner product.

the harmala.hcl salt resulting from manske is very stable and preferred for long term storage. the freebase is more prone to degradation but I didn't have problems storing it in a air tight jar in a drawer.

yeah defatting is unnecessary, I never encountered any fats or oils with rue.

the difference with dmt extraction is that harmala freebase freely settles at the bottom so it can be easily retrieved by decanting the liquid and cleaned with water washes. dmt freebase is suspended in solution so a solvent is needed to pull it out.