A lot of the mini-games do not contribute to your % total. You just get nifty stuff mostly.

Unfortunately the official guide isn't entirely accurate. The best I could get was 99% in a single playthrough.

I've heard that the easiest way to get that extra % in the next playthrough is to give the Awesome Sphere to New Yevon instead of the Youth League. I've also heard it's possible to get 100% in one playthrough, but only if the Youth League gets the sphere.

To get at least one of every item, object and GG, you have to do three playthroughs. Including ones where you deliberately fail certain missions.