I didn't understand (I didn't hear the sound in question that needs to be emphasized) so I didn't change anything as of yet.

03:45:897 (225897|0,225897|1) - I wanted this sound to be emphasized via the minijack, and removing the minijack and making it jumpstream would dumb the pattern down too much in my opinion. I'll keep this open in case there's a better alternative.

03:52:924 - This has lower pitch the three sounds that follow, but I didn't want a triple minijack so I chose to put emphasis on the two latter.

02:32:384 - This jumpstream is mapped to the pitch of the melody; I think some hand-unbalance is OK here to follow the music, especially since the pattern is not too dense.
02:33:465 - I had the same thought here initially, but had to dump it since the notes into the double (e.g. 02:33:600 (153600|0,153667|3) - ) are mapped to the pitch and three of them rise while one of them fall. It wouldn't be possible to have a perfectly balanced set of minijacks there, and I chose to follow the melody instead.

I couldn't make another pattern that does the same job (downwards at 04:08:600 - , switch to upwards at 04:09:681 - and have the visual contrast), so I just kept it like so. Variety is good, but I wouldn't sacrifice the pattern's job just to have a different one. Will keep this open in case I get a better idea.

If I were to map this, it would continue the previous pattern identically and would fail to shift focus to the next section, and would not distinguish the sounds before and after 03:40:492 - . Would rather have this part be empty.

Usually yes, but this sound continues the representation of 02:19:816 (139816|1,139951|1,140086|1) - which has the same sound on this column so I placed that note on the same column while shifting focus due to change in pitch.

Moved some notes from 4 to 3 to avoid the full anchor on 4.

I don't think this minijack causes a problem in this pattern; not enough to change it to a trill and go against the music.

I like having the non single-handed double on top of the triple since it continues the handstream motion whereas the 12/34 would discontinue the motion of the other hand along with the trill.