Aren't you the guy who made GunGirl2? I loved that game, and if I'm not mistaken, it runs smoothly with parallax scrolling and 640x480 graphics. It had some big levels too, so I'm surprised you ran into this kind of problems.
Just split your levels, man. a 8000x3000 level is kind of huge. Take a look at Super Metroid or other action/adventure games, they split their levels, you don't have levels that big. Every time you enter a door is like a loading time in disguise. So you have to do something like that. It will be a pain if you didn't plan your game to work like that in advance, but lesson learned, move on, that's how it is.
You have to learn how MMF works so you can go with the flow. Trying to force it to work your way is gonna give you serious problems. The software isn't perfect, but problems and all, I think it saves you lots of time in the end. That panda game looks cool too, so I hope you can finish it up

And sorry if you are not the Blue66 I'm talking about. Cheers!