Actually, I haven't gotten past the Stage 3 boss in Gradius III either.

I've been playing SotN alot lately... I think the % is at 94.5 (I still haven't gotten like half of the Relics or spells either), and I'm trying to get it to 99 before I go and pull out my can of whoopass on Richter. Getting those last few percents, though, will be of utmost tedium, though...