Hi
You do not want to put caps across the motor leads. That would be very bad. DC servo motors rotation is dependent on polarity, if you give it juice one way it will turn forward if you give it juice the other way it will turn backwards this is all done in the servo controller. If you put a big cap on the motor leads it could lead to an exploding cap and a fried servo drive. Most big caps like the one you are talking about are also polarization sensitive if you hook them up backwards they can explode, sometimes violently.
The cap should be after the bridge rectifier on the power supply, the smoothing that you are talking about is for the ac to dc process.
A motor repair shop is most likely only going to have ac start or run caps they won't have what you are looking for.
You need something like this
http://www.mouser.com/search/ProductDetail.aspx?R=36DY103F100CB2Avirtualkey61320000virtualkey75-36DY103F100CB2AWhen you measured the output of the transformer was that straight from the transformer or after rectifying (ac or dc)? If it is ac straight from the transformer then after it is rectified it will give you about 73vdc (52 V * sqrt(2) = 73.5391052 volts) and that would be just fine for your motors.
As for the encoders, you should use the ones on the motors.
Chad