Im 5-10 to 5-11 and have a 56 secteur and roubaix.
I used to get the neck and shoulder ache, I found it was caused by riding with my arms locked at the elbow.
Although this seems like it should be the most relaxing way, it does cause stress and tension. Best way to avoid it is to bend forward a little more, and bend you elbows and relax your shoudlers. It will take a while to get used to this as you will probably feel extra stress on your triceps and core, as they are now taking a bit more weight.
As for the knees I would guess that will be a saddle height and / or cleat issue.
If you can afford it a bike fit is a worthwhile investment. Some people will say its an expensive way of getting someone to adjust your saddle (theres WAAAY more to it than that!), but if you ask questions and learn while you are there then you shouldnt need to go again (unless you get a different type of bike. I had one from cadence sport, also had the footbeds in my shoes and really reduced my foot pins and needles), he also did the cleats too.