Thanks! I'm glad you liked it! I didn't get a chance to really fully try it out on Windows (I use a Linux Machine) or Mac, so it's possible that there are bugs due to that. I agree with you on the GameBoy palette depending on who makes it, so I tended to swap the palette a lot when I was making the game. I wanted to put in my own custom one, but didn't get a chance. The fade effect was something I was proud of. It was actually simple - basically, it's just a screen-sized sheet with each version having a certain dithering percentage covered.
The conveyors are definitely a known issue. I wish I had fixed it. As for the 1 and 2 flickering, that's not actually a glitch. That was intentional. It was meant to be like a geiger counter but wasn't sure how well that came across. (Geiger counters will actually fluctuate a lot around a given central value.)
As for all the other bugs you mentioned, I had actually caught most of these myself but didn't get a chance to fix them. I had to rush a lot at the end due to a vacation in the middle of the month and work preventing me from using the last few days. I might have to back and polish this game into a completed form. I have too many projects I want to work on and so little time, but hopefully I can go back and polish this up as well as another former project I did.
I'm glad you enjoyed it overall though and really appreciate the thorough feedback!