About a week ago I powdered 400g of mhrb and added it to 3000ml + H2O 300+g lye.

once it all cooled to room temp I added 200ml of vm&p naptha then shook and let settle 3 times in about an hour.
then with my home made Pipette I drew ~170ml then poured in a baking tray then freeze precipitated almost a gram of the whitest fluff I have seen in person.

I have been smoking the first pull for about a week and today decided to do another pull.

I noticed the remaining ~30ml was dark red and almost indistinguishable from the base without shining a light through it so I carefully pulled all I could out so it wouldn't discolor the next batch so I freeze precipitated it to get a red sludge with crystals all through it.
this didn't really bother me.

---Second Pull---

I added 150 ml of vm&p naptha and shook and let settle 3 times.

this time the naptha was darker than before, virtually the same color as the base but opaque.
I let it sit for 3 hours thinking it may be fine sediment material, it was no clearer.

just now I drew out as much as I could and placed it in the freezer.

any idea why I would get such dark naptha?

you put in way way way two much base.

take some water, fully saturate it with table salt then pour the water into the solvent and shake it like crazy, the water will pull out most of the red.

and add a bit of acid to the soup to bring the ph a little closer to normal, i dont know how much but the base level is just way too strong. start with two table spoons of 5% vinegar, and work up from there

dont worry the water wont take out any thing you want, but seriously that was way too much base.

also please refer to cybs salt tek if you havnt already, salt is your friend.

good luck.

3:4 ratio is not uncommon...

I have used the same ratio 3 times now with great success.

its been in the freezer for a few hours and a thick layer of brown material already precipitated out, I just poured the murky yellow naptha in a clean jar.

Each time I have seen a basified solution rest for more than a week prior to pulls, the case has been precisely as you describe, deep dark NPS yielding a dark red, gooey, active spice.
Having seen also the red d-limo pulled "jungle" spice, I would say it seems to be the same stuff.
My personal supposition has therefore been as follows. The extra alkaloids, oils, and whatnot which are pulled by full range extracting solvents such as d-limo, become more available to lower solubility NPS such as naptha, when the basified solution sits for a time. Maybe it is because this red stuff takes time to adjust chemically somehow in the basified solution.
It is interesting, and I have seen people purposefully wait the week or so to pull again, and yield the red goop to which you seem to refer.

from now on ill be more diligent,in my mind the week to sit shoulda been beneficial as the lye broke down all the cell walls.

I found a simple fix by basically doing a crude re-x with recycled warm naptha, let it sit for about an hour in the freezer and most of the sediment will precipitate out and be a thick goo, I then pour the remaining yellowish liquid in to a clean jar and continue to precipitate.

my pulls are small, I think this is due to the dye saturating the naptha, but The spice I am getting looks great.