Sorry for taking so long to reply... :p
The spikes that does not work will be fixed quite soon, the spot where you got stuck without gravity suit is also now fixed.
The morphball bomb timer was changed to mirror the one in MZM a bit more, personally I find it easier but that might just be me.
SpiffSpoo: there are actually two charge beams in the game. One is handed too you in case you manage to get to
Some parts of steamfair is accessed from other areas, such us Ridleys room and such. (Ridley is hard coded to be in norfair area, IIRC.)
Not sure why people have trouble finding Space Jump and speed booster. I can see if you have a hard time finding ice beam or screw attack, both are quite hidden.
The last terminal is suggesting that there is quite some hard things to deal with afterward, in case you want to go back and get some supplies before going in there, once you reach the aurora unit room you can't get back out again. The yellow circles are mainly only a reference to metroid prime 2! :3
I wanted to make it so that the planet did NOT explode, as it kinda does not add up with the story. But then I would need someone to recode the ending sequence, as that's something I don't have the skill to do myself. :/
Did you get that ending percentage from 1.24 version? If you're running on one of the earlier versions then it's normal due to coding error.