Some of what you describe sounds just like poor shifting performance because you are shifting at too low of a RPM/cadence and are having to use too much power to the pedals to keep moving. So maybe just shifting before your cadence gets too slow might help.

If the sprockets are in a different position due to the wheel changes, the clang might be that the side plates of the chain are getting hung on the top of the teeth as the wheel turns and then when you get to the strongest part of your pedal stroke the rollers fall into place giving you slack that is instantly taken up buy the crank. Did you turn the barrel adjuster to see if that puts the RD in a better position to complete its shifts faster?