I finally won, today! :)
To sum up the run: I chose a Thwomp in my first crystal room and had it go to town on enemies in the Forest and Jungle. My patience paid off. At one point, I had 85 crystals, and that's before I cashed out at the bank post-Jungle. So, I most likely topped out at around 100 crystals. I was able to invest a lot of that money in hearts along the way, which paid off due to some clumsy mistakes in the Desert, costing me around 6 hearts or so.
What won me the game was the Gardener and Storm (?) seeds for the final boss. Being able to create more plots combined with filling other holes with water allowed me the freedom to use a Thwomp to clear the area and maneuver around the missiles from above. That definitely brought down the difficulty, but considering everything I had done for the last 40 minutes, I felt like I earned that. :) I won't be expecting a run like that for a while.
Great game so far, devs! :)