You should have had better acceleration unless you timed the motor incorrectly.
Next time, do the mod without timing it just to see results one step at a time
The S2s with smaller pinions will still give you enough torque to use in small areas. If you are planning to do a swap while using the SB armatures(which give better torque than S2 arms) it won't matter which set you get since the pinions are all the same while comparing s1 and s2. If you plan on using the RS armatures, the s1 have more torque than the s2s.