First order of business to get shifting back in order is to check or have your derailer hanger checked and adjusted. The point where the derailer mounts should be in the same plane as the rim of the wheel. To verify if it is or isn't requires that the wheel be laterally true and properly mounted. Once the hanger is adjusted then you can begin RD adjustments. If the hanger is off plane with the rim then all RD shifting adjustments will be nearly impossible to tweek for flawless shifting performance. If you can't check hanger adjustment (requires tool similar to Park DAG-1) have your LBS check and adjust it. It is possible the hanger was just bent a bit or it may be worse and need to be replaced. Don't chance riding without the hanger being in good condition and adjusted as you will risk having the derailer go into the spokes and needing a new wheel and RD. That's not a good alternative and a bad risk.