I have heard theories that the causes are cotton fibres, fibres from other filters used, fungus, mould, or bacteria present in the environment which multiply in damp cottons, bacteria which are normally found in natural cotton, and others. Some say it is the bacteraemia itself, a sort of self-limiting dry run of sepsis, whilst others say it is an exotoxin which bacteria excrete and leave in the cotton,. Older cottons have more bacteria, more fungus, more viruses, and in particular, the fibres get brittle and break more easily. Allergic reaction to foreign matter is one of the more common theories about what causes this.
When it sets in, it pretty much just has to run its course. It does get less severe in subsequent cases and the duration can range from 15 minutes to 30 hours or so. Marked shortness of breath should not be ignored, of course.
The fever part of it can vary -- I have seen temperature rise to 42°C in the first few minutes, then go down to 39°C and stay there for the rest of the incident and return to normal over several hours after the remaining symptoms are gone. The most common sequelae are probably exhaustion and sore muscles.
I do know that using old cottons to compound shots in times of emergency increases the risk, which is why one perhaps should extract the drug traces from the cottons within 24 hours of use, concentrate the solution (use distilled water, not saline for the extraction because you will want to subject it to prolonged boiling both to pasteurise and concentrate the solution) and freeze it if it is not to be used right away.
Of course, for filtration, a wheel filter is the optimum. If improvising filtration, however, if you can find a filtering material which is hydrophobic and will not absorb the fluid that is better, and drug won't be left behind in the filter to any great extent for that reason, and there are not all these damp nooks and crannies for shit to grow.