I can almost Guarantee you that a Small bike @ 5ft 11" tall is the wrong size for you, for your LBS to leap from a small frame to Giant M/L is a massive leap. I would say it wasn't top service more like guilt. Top service would be to give you your money back or at least 80% PX on the bike they
wrongly sold you. He would have known instantly that @ 5ft 11 a Small would not be a comfortable ride. It really isn't a surprise that you are not comfortable.
For instance a lot of Cycle brands offer a rough guide for height to bike size such as
Evans own label
CX bike the small in this version is for 5ft 3" to 5ft 6", I would say this will be similar for most brands.
Giant size the CX bikes as race and commute . If you use the bike primarily for commuting then you go down a size if using it for for cx racing use your normal size.
I have used the shop before and bought a medium (Hybrid) and this felt fine so as I am using theCX bike 100% for commuting the advise was ,in theory sound,
It may be with hindsight (a wounder full thing ) that a medium would have been better.
And this is my point , ,I was given plenty of time to test ride .all afternoon if I had wanted to , the bike felt OK to me ,better that 2 specialized i had tried earlier and in the end it was my decision to buy.
I may have been influenced by the £160 off in the sale ,my fault not the shops.
But ,as I have said, lacking the experience of finding the sweet spot for a bike it really is trial and error .
I come from a cricket background and a bat bought in the shop can feel great ,on the wicket not so good, eventually you settle on a particular weight and balance and you can get it right most of the time.
I do not think it is a great idea to swap from shop to shop , they offer advise but that all it can be., hopefully working together eventually you can make the right choice.