Well, after watching my movie for about the 50th time some things are starting to become clear. I'll post those here for a time when and if I (or anyone) wants to improve the run. Here's what I found:
In 1-2, the last trampoline could have been jumped off of better because the drill clips the ledge. I believe if I moved to the left a bit before drilling I could catch the ledge without clipping it and be a few frames faster.
In 1-3, I'm sure the drills on some of these platforms can be better. Also, when falling off the last star platform I could have ran to the right when landing so as to avoid the landing animation which takes up a few frames before allowing Aero to push the cannon.
In 1-4, some of the ledges can possibly be drilled to earlier in the seesaw section.
In 1-5, (untested) sometimes it is probably faster to drill to the right when coming off a ladder.
In 1-B, I'm sure the last drill could have been drilled into the bottom of the stilt brother allowing me to instantly drill to the right. However, the stars often times don't let you enter them until a certain frame anyway so it might not be any different.
In 2-1, it might be faster to drill up onto the second star platform. Also, if buttons could be manipulated to be out of the way of the very next ladder sequence, Aero could drill downwards off the ladder instead of going down it a few frames and drilling up. That stupid flying helicopter man in this level seems to always want to swoop down as I'm passing, maybe that can be manipulated as well.
In 2-3, I could gain momentum from the fall on the part preceding the cannon by moving left and right. I seem to have continually pressed right against the wall the entire time. Also, I want to experiment more with the cannon shot, as I think it would be faster to shoot at max power and then drill onto the ledge. Another annoyance with the little dude later on where I have to drill down to avoid him, perhaps he's manipulable. This next part has been bugging me for quite some time: I realized I have 3 unused stars at the end of the level that I could have shot at something.
In 2-5, the first spiked post in the trampoline section can probably be drilled over quicker. Maybe if I dont clip the ledge after the two-part ferris wheel section, I can keep my momentum up. The little dude on top of the hut later in the level was also at a bad position where I couldn't jump up to the platform above and into the ladder sooner.
In 3-1, the part coming out from the tree (when the direction of the level turns to the left) I believe I could have jumped on the little floating land with the flagpole to avoid such a slow uphill run. Thanks to ShadowJacky for pointing this out: It is possible to skip the seesaw in this level by jumping from the tightrope straight over to the ledge.
In 3-2, there's no real improvement here but something I wanna try: I wonder if you could jump between the spikes on the second one where there is a small gap between them and then back out again. I tried the first one, the gap wasn't big enough. However, the next gap seems to be a bit wider.
In 4-1, I may have stayed on the spiral platform too long before jumping off, as it seems to stop a few frames before I actually jump. Some of the drilling in the trampoline section with the spiked posts can probably be done sooner. Also, I just want to do some overall retesting of that last section with the fireballs.
In 4-3, I'm not sure if landing on the buttons statues is faster in some places, as you can only accelerate on the ground, this prolongs time spent in the air.
In 4-4, the first electric tightrope could probably be faster by drilling off every jump which seems to be faster than just jumping. I do it for the second one but not the first for whatever reason. I really wish there wasn't a reason to slow down for this stupid ghost, but he is very annoying.
In 4-5, I wish there was a way to catch these rotating spikes so that I don't have to drill and lose momentum on two of them. I have a feeling if I change anything in the previous parts of the level, those walking spikes on the floor at the end might prevent me from cleanly jumping over it.
I think the final boss can be improved overall, perhaps he can be manipulated at the end to not shoot water in the way of hitting him (the direction of the water seems to depend on the position of Aero).
Again this is all just for future reference as I probably won't pick this game up again for a while, or maybe who knows.
Current thoughts:
Hachiemon (J) for GBA.