I used to feel really sore the day after a hard workout but now i don't feel it as much but i'm working just as hard. I have tried increasing weight/reps and amount of workouts per part but i'm not getting the same soreness. More tiredness/stiffness with some soreness. Does this mean i need to change something in workout or is body simply getting used to it?
Actual soreness will decrease as your body becomes accustomed to the movements you are doing. If you keep the intensity up you will still become fatigued with some soreness. It sounds to me like you're doing well.
What are the differences between what you are doing and the waterbury method?
Doesn't sound good, perhaps not take off but ammended workouts would be wise. ie, spinning, biking, jogging (if doesn't cause pain), lower body lifts or machine assisted lifts.
Don't stop just modify, it helps to stay in practice.