Any help to fix him will be appreciated.

Ok....Dogs flick their tail when they are hitting their back legs while running ....Most often the rail side hind.....Possibilities are railside metacarpal trauma [depending on age]....Railside Triangle or hip support trauma or perhaps the offside...[not so often]...The reason that he is showing soreness in the shoulder and resisting you is that he has been desperately scrunching up his flank and shoulder when galloping to try and avoid hitting himself....If you can imagine running down the road and someone has a little hammer periodically hitting you in the shins....Takes away the enthusiasm a bit.....These are the most obvious reasons Ivan but I am sure others will elaborate further.
Very hard to diagnose long distance.