If I missed it, how many miles are on the clutch? Organic disks are kinda mooshy sometimes while they bed-in.
As long as you know you are completely engaging the clutch (it sounds like you are - point of engagement near the floor is a good sign. If you check the cable at the fork and have a hair of slack in it, you know you're as loose as can be), you have done all you can.
If the break-in is proper and this doesnt go away after the break-in, contamination or a bad diaphram fingers could be the issue.
Good luck.