In step 1, mix until the salt has dissolved and the bark is well mixed in.
You should be able to just mix by swishing with the amount of spare volume in the flask at this stage.
In fact, I never use a spoon at the NPS stage, I just invert the flask ( I have a glass stopper in mine and keep my thumb over it ) about twenty times, in a steady non frantic rhythm, so that the NPS and base get mingled thoroughly. Then wait ten mins or so for it to separate and start again.
If I've warmed things, then I'll be aware that mixing can introduce the NPS to hotter liquid and cause vapour pressure to build, as it was warmed from the bottom of the flask and the NPS is sitting on top.
So I'll carefully 'burp' the flask before and after the first inversion and after each inversion until I feel no pressure from NPS vapour any more when I loosen my thumb from the stopper. I wear rubber gloves for this as the caustic soup is liable to spurt out a little if not careful. To minimise this, let the flask stand upright for a few seconds so there is less soup around the stopper. Also just don't let it get too hot, and definitely not anywhere near the boiling point of your NPS.
The nasty scenes of dye covered kitchens you may have seen must have been from screw lid jars being heated too much with low BP NPS in them I reckon.
It's amazing how many details suddenly seem important when describing something isn't it!
Anyway, the above is my way of suggesting that stirring for two minutes may not be mixing the NPS into your base soup enough as you seem to be getting very low yields. Shaking it vigorously can give you an emulsion, so try in between as described above.
You seem perhaps a little fixated on finding the "one simple true way", but, as with life, there are several routes, each with their own drawbacks and advantages.
For instance, you can (eventually) get all the DMT out by mixing the NPS only slightly, it's very emulsion safe, but will take many pulls of smaller amounts of NPS to get there as the surface area of NPS in contact with the base is minimised that way. Shaking vigorously will maximise the surface area of NPS in contact with base, but can lead to emulsions so the NPS won't all settle back out again. So go somewhere in between
Good luck!