Hey Kayse,
Thanks for posting.
So the best tool to flatten out the leftover thinset is to use a grinder wheel like this dewalt one:
https://shop.bathroomrepairtutor.com/collections/tile-tools/products/dewalt-dw4774-4-1-2-inch-double-row-diamond-cup-grinding-wheel
This is a fairly dusty thing to use…..so have a shop vac near by and/or purchase a dust guard for it. https://amzn.to/2GS3kf7
Minor low spots. I would recommend using a floor patch like this:
https://www.homedepot.com/p/Henry-547-25-lb-Universal-Patch-and-Skimcoat-12158/100189852
If its really bad and you don’t think simply patching areas will work, you could floor level the entire bath if you can afford the space.
Normally you want to have a minimum 1/4″ when floating the floor with leveler, anything thinner will make it tough to spread.
I really like leveler from ARDEX, but most levelers at the box stores work great if mixed to specifications.
It sounds like grinding and patching might be all you need though And if the low spots are under a 1/4″ I would simply fill with thinset when installing schluter ditra. (if that’s what you plan to use for under tile)
Any pictures could help to evaluate the situation.
thanks