I think we need a little clarification to understand how to better help you.
But let me see if this clears up some thoughts
1. D-limo and Naphtha are miscible. It would be very hard to actually separate them with out proper chem equipment, ie a column, centrifuge or something along those lines. Not very practical for a kitchen chemist.
2. Usually when working with D-limo, people will use an acid to "salt" the DMT from the limo. There are many teks about this, and i suggest searching the forum for back salting or FASA precipitation. Freebase DMT does not precipitate from D-limo in the freezer like it will in Naphtha.
3. Either precipitate DMT-fumarate via titration; or plan to backsalt to an aqueous mix and then base with a strong base to turn back into Freebase DMT, and then do new pulls with the NEW Naphtha. The freebase DMT can then be precipitated in the freezer, and will have minimal D-limo contamination. you should still get crystals even if there is a tad of Limo in there.
4. After that, you can do a series of cleaning to the product, involving filters and/or re-crystallization.