If you want, a simple, spoiler free and hinting instead of outright answering guide to getting all the endings read below.
Good Ending?: Complete the game without achieving any other endings.
Bad Ending: Fall at the last hurdle.
Secret Endings 1: Find the secret files, input the secret code you get from looking within instead of the one the game asks for. Make a choice at the ending.
Secret Endings 2: Find the secret files, input the secret code you get from looking within instead of the one the game asks for. Make a different choice at the ending.
You're welcome. Getting the bad ending is easy, getting the two "true endings" is more difficult and requires some esoteric thought processes. I am quite proud of how I've hidden the important passwords in the game.
If everything is working correctly and you haven't found some previously unknown game breaking bug the following should be how you get through.
Spoilers:
I imagine it's not the most surprising to learn that any obstacle in the game that gives you multiple chances before seemingly killing you arbitrarily is actually dealing damage to your health. The death state of the obstacle is engaged when you interact with that obstacle and your health is dropped to 0. The second area, especially combined with the first is designed to be impossible to cross with your current health.
However the vending machine in combination with the coin on a string you should have gotten from the research area allows you to restore your health to full which should allow you to get across provided you don't take the wrong path.
Assuming everything is working correctly, you should just have to interact with the vending machine. If that doesn't work... I'll ask you to provide more explanation on exactly what you're doing that is causing this to see if there is a bug in play.
Locking the funniest possible answers behind your flappy bird score is the most evil genius thing I've experienced in a while... I played the flappy bird of my life so I could say the words "ram into my pipe Flappy-Kun!!!"
I meant to include in the dev log, but forgot. I don't know how to draw, I had an artist friend who was willing to do some work for me, so there are a few custom sprites in there, but part of the planned aspects of the expanded game I eventually changed my mind about was going to be, proper pop out artwork for the various monsters and certain scenes, but my artist friend who was not being paid, got busy and couldn't continue and since they had been so nice and doing it for free up until that point, well I decided to just go without art. I don't have the money to pay an artist at current, though hopefully I will be able to hire a proper artist for any future games.
