Actually, I believe that the ending maze is semi-randomly generated. For me, the final room was pretty close to the middle of the map.
That said, you need to clear out all the fights before that vortex door thing opens up.
As for the % complete, I'm pretty sure that the extra % comes from going back through some of the other stages. For example, when you go through previously visited stages to get some of the secret characters. After doing some of that stuff, I'm around 85%.
Also, maybe I missed a trophy somewhere, but for some reason Ike and some others disappeared from my lineup.