Sounds like to me you have lower unit issues. If it starts and runs OK in neutral and is hard for you to put it in gear, then likely you have gear issues. If when you start it and runs rough and make bad noises then its likely to be powerhead issues. Though, from you description, it sounds like a shaft, bearing, gear issue. Take it to Bowden Marine and let William take a look at it. By the way, when in neutral, can you turn the prop by hand?