Okay - You want to feed coins in and count a certain amount into each stack and any extras go into a separate bin.
Here's an Idea - the coin starts in - Have some form of light detectors (opto couplers?) that detect the coin and its size. For each size have a servo - servos all retracted will send all the coins into the extras bin. As the size is detected, and the count is less than your limit, activate the servo for the proper size coin and it will be tripped into the correct bin. Also use a servo at the start to feed the coins on at a time. Might check the size before the coin is released by the first servo to give the other servos time to get in position. You could use either time or a sensor in each receptacle to tell the machine when to release the next coin.