To start, make all these pin assignments byte instead of int:
//const int loadTime = 100;
const char PacketStart = '~'; << not this one, but the rest
const int portBow_Dir = 2;
const int portBow_PWM = 3;
const int portStern_Dir = 4;
const int portStern_PWM = 5;
const int stbdBow_Dir = 7;
const int stbdBow_PWM = 6;
const int stbdStern_Dir = 8;
const int stbdStern_PWM = 9;
const int vert_Dir = 12;
const int vert_PWM = 10;
const int manip_Dir = 13;
const int manip_PWM = 11;