I haven't watched your movies yet, but here are answers to many of your questions.
Regarding crashing the game in wily4 according to your description, yes it is related to how Shinryuu also crashes the game there. Shinryuu's scrolling moves both the physical and visible screen to point to nowhere, so the game crashes. Your trick brings only the physical screen to that void, but this is sufficient.
There are a lot of files in your zip. Can you tell us which one has this crash bomb glitch? That sounds like a key innovation here and it would save a couple frames on that bossfight. However, it won't save time on later boss fights because crash bombs are not used afterwards.
The following bosses have been seen to get glitched graphics after doing heatbug (a misnomer that refers to left-scrolling in the boss room):
airman
quickman
metalman
mechadragon
alien robot
As far as we know, the following bosses can be damaged but are not visible after scrolling:
heatman
woodman
bubbleman
flashman
The only boss that retains his normal graphics after the screen scrolls:
crashman
If you really want to ask why, there are naturally some characteristic variables (palettes, tile tables, etc) to define the graphics in each boss room. Boss fights weren't meant to go through room scrolling, so these variables can get messed up in the process since the programming might depend on them not changing before the end of the boss fight. I can't yet offer any deeper explanation for this nor as to why most bosses end up with the single-hit corner while most don't. And likewise with the room-shaking points.
The item3 trick that Shinryuu and Omega are talking about is something else. We don't yet know a way to use item3 in place (except when you're up against a wall).
I haven't figured out a way to cross the pit without item1. The page that Shinryuu linked a while back has some pictures beyond that point, but since I can't read Japanese it's not clear to me whether that guy used cheat codes or not. If you'd like to see a video of what happens past there, watch this:
heatbug_finish.fcm. I created it by patching in item1.
Shuttertech might not be fully understood, but through extensive testing we now have a pretty good idea of where it can and can't be done, and know the various points where it would be done in Shinryuu's future run.
A "full amazing run" for Rockman 2 could be pretty cool, but unfortunately it's also an enormous challenge that isn't any easier than the standard TAS. In addition to glitch worlds it would require almost all of the tricks shown in the regular run. Many of these techniques are very difficult to pull off optimally, and right now the regular run alone seems to be quite a handful.
Yeah, it would really help if you could run FCEU. That would allow you to watch some of the movies in this thread and better see what we're talking about. Also, you'll probably have an easier time making movies in FCEU rather than Nesticle and then we'll have an easier time watching them.