The burning smell may have resulted from tapping the coupler too far onto the shaft of the motor or tranny. This causes the back side of the coupler to rub against the motor or the drive lug of the transmission. The odor gradually dissipates as the affected area wears away and the motor is not under duress due to binding.
The pump leak is purely coincidental, but could have resulted when it was disconnected from the motor during the repair. If you did not disconnect the pump, but rather dropped the motor & pump as one unit, then it could have been bumped as you said, causing the seal to leak. Go ahead and replace the pump.