Banana coins respawn, so I'm not sure if that would be possible to track between sessions. The most you could do is use a mem-delta and actually require the player to get ALL of them in a single-run(with no savestates), which could potentially be cheesed if there isn't a proper ResetIf. Coins are rarely in difficult to reach areas anyway, it would basically just be a 'go look at a FAQ' achievement that would take several hours to do. And hardly any point value would be worth doing all of that when there are so many other things in the game to keep track of. I think at worst, maybe care about banana coins for one achievement for reaching a generic-amount. ..but really, I think the things you buy with them would be more interesting than just-getting-them.
Rather than keep track of the actual percentage, which would probably be redundant(as in, you would be getting an achievement for 'getting all achievements'), it'd probably be best to keep track of the individual parts that make up each Kong's collectibles. For how many levels there are, it would probably be best to keep track of each Kong's all-game collectibles rather than per-level, and only care about per-Level-collectibles for the stuff that isn't tied to specific Kongs(like banana fairies and battle crowns). Also ignore Banana-Medallions since they are awarded at 75 bananas when you could just look at them having 100 bananas per level for all-game(per Kong or all Kongs). Most of the story-progress could be tied to boss-battles, no-damage bosses might need to be tied to boss-rush(and hopefully per-boss and not just ALL-boss), and maybe have one achievement for the first and last upgrades like Health and ammo..otherwise having every single upgrade per-Kong would be a huge amount for no real reason.
The more I think of it, there will have to be a lot of careful balance in achievements for this game because of the potential for it to either be a huuuuuuge list of achievements for no reason, or possibly so compacted that you wouldn't get a single achievement for hours depending on how it's handled.