The two main ways of influencing differential cooling are to change the cooling channel layout, or use mold inserts.
Perhaps one of the easiest things to alter is the temperature of the coolant. It may be useful to run two additional Cool analyses with the coolant inlet temperatures at say plus and minus 5°C with respect to the original inlet temperature used. The results from the Cool analyses can then be used in a single variant Cool analysis to give you some idea of the sensitivity of the part to variations in coolant temperature.
If it is not sufficient to simply alter the coolant temperature, you can consider the addition of extra cooling channels in troublesome regions or the use of mold inserts to reduce variations in cooling rates across the part.