Problems after replaced engine?

Engine replaced? Perhaps engine and transmission as a unit? Check number of teeth on engine/trans output sprocket- you may have a more tooth/high speed drive sprocket and need to move back wheel forward a bit. Spongy shock? Does the spring have a load adjustment bottom retainer- a circular cam arrangement? perhaps it was turned to lightest load setting. Or you put on some weight? Rear springs can fatigue, shocks don't affect load bearing unless they are air or gas charged for extra load bearing.