First of all, did you get perfect scores on all of the boss bonus games? I don't think simply playing them is enough. Aside from that, all I can think of is that you haven't rescued the girl blob, but that shouldn't be worth more than 1%.
Language is a tool for efficient communication. The Internet is a tool for fast communication. Don't defy both intents by posting incoherent writing.
I just got a 100% today after watching a YouTube video of a 100% speed run. They got a perfect on all the bonus stages, so I followed suit. That netted me 99%. So I went to stage 2-3 and used Kine just like the FAQ said, but they were wrong. I think they meant to say Coo. Anyways I got the girl blob and that got me the perfect percentage! Sweet! Thank you for your answer KirbyManiac.
Big thanks to this topic for getting me that last percent, but COME ON HAL LABORATORIES! How on Earth would I guess that rescuing a girl blob when I'm using the owl is going to net me an extra 1% completion? DUMB!