The Legend of Zelda: A Link Between Worlds Discussion

I'm currently trying to find each and every one of the Lost Maiamai. So far I've located the ones in Hyrule, and now I'm searching across Lorule for the others. But there's one thing that's bugging me: how in the worlds did half the Lost Maiamai end up in Lorule in the first place?! It's mind-boggling!

I'm at the final boss and am having some trouble

I somehow managed to scrape through and beat the final boss, but I can't remember how I did it. It was a while ago.