If you're knicking the prop on landing, then it doesn't matter what the clearance measures, it's not enough for the landings you're going. If you're flying off of pavement, it's not odd to knick props. But you didn't mention the trainer. It must be a taildragger, so stop trying for a three point landing. That'll give you some time to get used to controlling your landing speed better and once you've got that down pat, you can go back to working on getting the flare right.

BTW, don't work so hard on the flare. When the airplane is about to touch down on the mains, just pull off the remaining throttle.

One thing to look at closely is how your landing gear is working. Has it spread out? Most trainers' gear can be bent somewhat. Try bending the gear in some. You'll bet more clearance AND a bit more stiffness. Sounds like you could use stiffer gear. And taller gear is probably available at your LHS.