I haven't used the Shimano R650's but I expect they would be very good. The Tektro R539's I can tell you are simply excellent. Either of these would be a great choice. You might also consider the Tektro R559's since you're right at the upper limit of the 539's. A bit of wiggle room is often useful.
For levers, have you considered something used? The Tektro RL520 levers are for linear pull brakes and won't work well with the calipers you're looking at. The Cane Creek SCR-5 work well, but for less money you can buy an old set of Shimano SLR brake levers that will work as well or better and depending on your tastes may look better on your bike. I've got a bike with 105 levers (BL-1051, I think) and Ultegra BR-6600 calipers (similar braking response to the R539, but less reach) and they work wonderfully. If you really want something new, the Shimano BR400 levers are a modern version of the same basic design.