Is it possible that the rod from the booster to the pedal is not set at the correct length? It is very easy to adjust by moving the turn buckle that hooks to the pedal closer or further away. Since it costs nothing and takes little time to do it, I'd try moving it. You want to be sure there is some free play in the pedal but too much play may be a problem. You might want to google making this adjustment as there a number of posts on this and you may find someone has documented the swap you made. Perhaps there is some other adjustment needed. Best of Luck!