To answer chronologically:
1. I've seen some people doing it in a shot glass ? Why is this? Why not in a glass baking tray like the pulls
Well the overall structure of the glass totally does not matter. The whole process is just: Reduce the volume, that it will definetly start crashing out upon freezing and then start freezing it. If the crystals attach to the walls, simply decant everything off - otherwise keep attention that you will not pour out crystals while decanting.
There is no special reason for that shot glass - possibly the volume of the solvent was pretty low and those guys wanted to use a tiny glass for that tiny amount - but any glass is equally good, I would do it in a bigger glass as it is then much easier to scrape out all xtals.
2. is there a benefit to combining them together rather have individual pulls 35ml in separate trays
No there is none - it is just that you only have to handle 1 glass instead of (let it be) 5. If you want to check what pull contained what amount, then you should do it 1 time each on his own. Then you know: Pull 1-5 was worth it, pull 5+ was not worth it.
Then you can stop doing more than 5 pulls the next time.
If you already know this of for any other reason you dont care how much was in each pull individually, then just combine it for more easiness.
3. when filtering the matter gets gloopy when in the coffee filter and becomes impossible to retrieve
My thoughts on this: If the material is orange, then it is Spice contaminated with other unuseful plant compounds. Those plant compounds will be hard to viscous when frozen at - 20°C. But upon warming (like when you try to filter them) they will become more sticky and then it is impossible to get them out - that is true.
My advice: Do NOT try to filter them, try to slowly separate as much NPS from your stuff as possible and try to decant the rest of the NPS with the sticky stuff on a flat plate. Then let it evaporate - not the filtering way.
The sticky thing will also become more slimy, but then you have it isolated on a plate. Then you can do whatever you want, but possibly it is too unuseful to handle so you could directly dissolve in acetone to make Changa - but again: dosage is not precise.
You can wait to it will harden on that plate eventually after some days (in the dark of course). Then you may handle it better, but that is not sure.
Lastly:
If things are floating in your NPS after pulling, this seems strange to me. Normally directly after pulling there should not be anything solid in the NPS. If you heat the NPS while pulling (which I highly recommend) then something starts precipitating, as the NPS will cool down after the separation. Therefore this will start forming solids if you wait long enough for those to precipitate. But directly after the pulling procedure it sounds strange that there are solid things floating on the surface.
Maybe post a picture the next time to check if its dirt or useful.
If there are ONLY Crystals on the bottom (when you wait in the freezer to precipitate) AND on the surface but none inbetween, then you can use a pipette to remove the solvent in the middle of them. This way you will be able to get out 90 % of your solvent if you use a high but narrow glass, and you will not loose the stuff on the surface nor on the bottom. Then those stuff with the residual 10 % solvent could be placed on a dish to let the solvent evaporate. This would keep you all stuff which you think may be useful and you still have nearly maximum purity (spoken by the freeze precip + decanting method).