I think one of the bigger things that's throwing off the perspective are the roots on the far left and far right sides of the tree--- they seem like they should be further back. I'd also suggest making a light color outline for where you want the trees peak to be, and sprite using those guides. That way, you can almost guarantee it's going to fit in. From what I can tell, it's not so much the placement of your apex and such for the canopy, but it's how far back they actually go in relation to the trunk. If you roughly match your proportions to the guide I made, it should look fine with the perspective.
