Just one question: What frequency are you trying to use the amp on? Voltage mode class D doesn't work at HF, it might be ok for 160 meters and definitely works for low MF and LF, but at HF a current mode class D amp works better. If you look at the old class D information that Jay had on his website (found here:
http://w1vd.com/375wattclassDold.html ) he originally tried voltage mode for HF and ended up switching to current mode because it didn't work. Also which drain waveform were you measuring? Voltage or current? If you are in voltage mode, the drain voltage should resemble a square wave and drain current should resemble a half sine. Current mode is the opposite, voltage is half sine and current is a square wave.