The whole colourful spectrum is most likely caused by the various other alkaloids that are inside the MHRB. Naphtha isn't a very selective solvent so it will dissolve the various other alkaloids inside your solution. There are various colours of DMT, ranging from pale white(as is seen mostly these days) to slightly yellow, orange yellowish and dark red. A lot of people will refer to red spice as jungle spice. I remember seeing a very thorough guide done using various extraction techniques to determine when which colour is taken by the spice.
There is no need to let the naphtha layer separate at 95F for 12 hours. That is WAY too long. Your naphtha will most likely have evaporated(although 50ml seems like quit a bit) and part of it is probably still in your solution. Next time you do an extraction, heat your soup to around 140F / 150F, tip the naphtha in, mix thoroughly and then let separate for about an hour and then siphon it off.
As far as the dark 'specs' in your naphtha layer: that is probably just mhrb particles. Could be caused by disturbing the naphtha layer by moving it.
The spice extends life.
The spice expands consciousness.
The spice is vital to space travel.