I've been playing build 41 for about a week, and I've been struggling to make contact when stomping . This is a serious issue in my opinion because the goal of a survival game like this (like Don't Starve, the Long Dark, etc.) is that you should be learning from each death. I take notes each time I die, and the clunkiness of the stomping mechanic has been the cause of 12 of out my last 20 deaths. As far as I can tell, the only lesson I can take from this is that I should avoid stomping as much as possible because it is very clunky. But that is hardly a realistic lesson when combat is almost unavoidable in build 41; and why should the developer add a mechanic, only for everyone to avoid it because it's implementation is clunky.
Knowing when my player is positioned on top of something was always a bit of an issue. Even in build 40, I would sometimes struggle to position my character on top of something sitting on he ground (like a car key). But now that this clunky mechanic plays such a critical role in combat, something needs to be done to improve it.
My suggestion should be simple to implement, and would not significantly alter the game's balance: Add a context indicator to let the player know when a stomp attack is going to connect (think of the "attack" indicator that shows up in Don't Starve). This could be as simple as making the circle reticle that was added in build 41 turn red when you're positioned in a way that if you left-click, your stomp attack will hit the zombie you're standing on.