Thanks for the heads up about the accessibility of the AIN0/AIN1 pins. I did some more research and the AIN1 pin is accessible via hardware. However, the AIN0 pin is not accessible by hardware. There does appear to be a way around that problem with software. The analog comparator has the Digital Input Disable Register 1 (DIDR1). Bit 0 disables the digital input for PE2 (aka AIN0). If I don't disable the digital input of this pin and set it to output high or input w/pullup enabled, that should put +5 volts to AIN0. I haven't tested this yet. I'll update this post for anyone interested in using the analog comparator on the Mega.