I found a way to save four minutes off the Green Beret jungle section by alerting and desyncing the Green Beret:
https://www.youtube.com/watch?v=obov9q0odIo
This may be able to save time for a speedrun of the Virtual Console version, but I am not able to test that version on emulator. Can someone else please test this? There are two things here: 1) Moving to the next screen must be done at the same time as Green Beret. 2) The punch in the upper left screen(second punch) must be done right before he changes direction in that corner. That is what causes the Green Beret to desync. The first and last punches are done so that Green Beret does not outrun Solid Snake.
I also found a way to save a couple minutes on the egg by using a deathwarp, and also the deathwarp can be used in quite a few places to save multiple minutes.
I have been busy planning the route, but because drops are on a running timer that does not reset, I am unable to make a test TAS that will reflect what the final will look like. So I decided to start the actual TAS and hope everything works out. I just got done with the Black Color fight, which looks cool.
https://www.youtube.com/watch?v=qFIPf2Okt5g
I found some other miscellaneous stuff as well:
I can make a guard float off the screen.
https://www.youtube.com/watch?v=jSfWXLGcpXc
The game gets confused when doing a double KO at the end.
https://www.youtube.com/watch?v=ShfAvoK1Qlo
Speaking of getting confused, how about a game crash?
https://www.youtube.com/watch?v=R3AfDV89_H4
Here is a glitch in the swamp, but is not useful unfortunately.
https://www.youtube.com/watch?v=y4ELJMrwzvo