Lots of people use Windows on MBP for gaming, however the placement of Left Alt key and left Window key is quite annoyin for its difference w/ windows keyboards. Just wondering if there is a way to reverse the function so i don't accidently pop game back to windows desktop while gaming.

System Preferences -> Keyboard and Mouse

You can also order the left side function keys any way you want with the MacBook Keyboard settings dialog.

What is the "Pause" Key on a MacBook keyboard in Windows? On my home machine i thought it was F7 or something like that, but now i sit at
another MacBook and just installed Input Remapper and it doesn't work.

I don't believe that Input Remapper has the pause key in the MacBook keyboard settings dialog. You could add it manually though.