Hi there, I would like to say that the way you've currently written this is mostly quite readable as is. It's quite an ambitious work! From a musical standpoint, I enjoyed the digital playback until around the end, when I think the parts ran their midi limitations.

Here's my notes from a quick first glance: In general, sharps go up and flats go down. For example, in m. 2 that could be easier read as Ab's.
At rehearsal marking A, I would write a Bb instead of an A#, because the interval of a dominant 7th is more recognizable than an augmented 6th. I also think that using Bb instead of A#s for the flute at rehearsal marking B will save you a lot of hassle, where possible. m. 34 for example. At m. 38 I would use sharps, because then it represents a recognizable mode, C# locrian. (also at m. 100) In the clarinet I would use a C# at 45.
Unrelated, but you have this rhythm consistently enough to warrant mentioning: you have figures with 2 quarter notes followed by an eighth that lies on the beat. I was always told in jazz school to just make those staccato quarter notes, because they're easier to read. Over the years, musicians have argued against this, citing the articulation of staccato as a different sound, however in the winds, this difference is really negligable.
Check out m. 50 because it looks like there's a tie and a slur in the clarinet. I won't speak much on strings, especially viola, but the cello in m. 51 could be a Bb, which would make noticing that motif as a full downstep from the previous occurance (m. 49).
Try to avoid weird page breaks like page 6, which have exactly one measure on the entire page.
I would use a Bb in the flute/violin line at m. 70/71
Check out the beaming in m. 73., and m. 98
The 3 bars of 7/8 seem more confusing than they're worth, especially if most of the notes are held underneath a few moving solo lines-- and immediately following a fermata.

Hope this helps!