Deleted a few more unused variables, cleared a few compiler warnings mainly about passing incompatible variable types and casting issues.  Also added some more comments about the main loop and the general operation of the system.  Threw ISRs down below main().  Still getting compiler warnings about ISR priority, so far this hasn't been an issue but I should probably take care of that at some point, espcially if we ever have multiple ISRs interrupting each other.