Improvising and composing fusion are two different ball games and the former is a much easier one since the interesting chords are already there, and aside from some potential difficulties phrasing from one tonality into another dependant on the oddness of the chords underneath it tends to be standard analysis of tonalities and into subconscious phrasing mode (assuming you've programmed your subconscious in the usual harmonic and melodic tradition - anchors 3 and 7; 1, 2, 4 and 5 pentatonics; dominant tritone scale on dominants, chromatic sidestepping etc. In a nutshell, all the usual tricks, and if you hear something that sounds different and cool transcribe and assimilate it.
But how do you come up with chords like that in the first place? How do you compose Havona, or Looking Glass? I found a state of thinking that was really useful - in all places - in learning Giant Steps (on the piano). I found that if I kept consciously thinking the II-V-Is in each key and the major thirds I would get bogged down in thinking, whereas by thinking more "da-da-da-da-daaah" without the theory clogging my mind I found more fluidity. This non-theoretical thinking is especially useful when composing odd chords since I find I don't constrict into diatonic or substionary categories but rather allow for harmonic possibilities to suggest themselves.
Kind of fluffy, but I hope it helps.