That's odd. All secrets, treasures and toppins should add up to 100%. Achievements and P ranks should only add up to the extra percent to go all the way up to 101%.
Clothes carry over between files and do not count toward completion in any one file.
Maybe check the computers in the hub? They run a tally on all you've collected.
That one missing S rank should bring your file completion percentage to about 98.8%, which then gets rounded down to 98%. Could you put the P ranks aside for a second and focus on that one level?
Moin,
after the shocker that was today, we'd oughta bring you up to speed (lol pun) what's been happening the past day for Swap Mode.
A major trick was discovered for Swap Mode (1P and 2P) titled
In short on how it works: In Swap Mode,