There seems to be an issue where there aren't enough slots for the clear all preset with K2SE.

that is possible. there is a hard limit on the number of requests a character (or any entity) can have.
if K2SE adds too many items, then that's it at the moment.

actually this is a dublicate of Please add option to trash unrequested items

Would a possible workaround be to trash items that are currently in inventory and not requested and just add those to the 0-0 requests?

at the moment you cannot modify the predefined presets - sorry.
But of course you can create 0-0 request manually - they will be saved along with the other requests you have, if you update or create a user-preset.
Other than that you can of course simply put unwanted items into the trash-slots, that should work by shift-clicking them while no entity but your inventory is open.

I just published a new version of the mod that should help with the too many items-problem.

I'll close this, please have a look at the linked topic in my first response for updates.