At first seeing Kraid's room I thought he just needed a reassemble which is no prob. at all, but there are so many rooms messed, even the first missile room. I wasn't even able to get to him from the ship, sorry but too many things are in bad shape =/
i played around with it, couldn't get to kraid from the ship either, so i savestated my way into the room before Kraid, and edited some of Kraids values. Got the room to work, except you can't touch or shoot at kraid at all. After that, anything I tried made it worse. I suggest starting over, and not changing the # of PLMS/enemies