Having been solely on PowerCranks for 8 days and 10 sessions, I have made a few alterations on my bike to make riding more comfortable.    
Being unable to unweight yourself or bunnyhop on PowerCranks, all bumps and cracks in the road surface can be felt up through your saddle and handlebars.
It seems like the headset takes quite a beating every time you hit a pothole - according to the loud crunches - or maybe my headset just needs to be replaced anyway.
On my winterbike I´m riding 28 inches clincher, Continental TopTouring, which are literally bomb proof, and besides giving good protection from punctures, they make for a very pleasant ride as the greater airchamber acts as a bumper.
I´ve changed my original Selle Italia "Flite" saddle to a more cushioned MTB saddle from Specialized and I think that I can feel the difference in my "sitting area" already.
My next, more drastic, modification would be applying an extra layer of handlebar tape or actually the closed foam tubes you use for insulating waterpipes in your house, or as a lightweight mount for your heart rate monitor.
My last three rides have been on the hometrainer and I´ve been experimenting with intervals incorporating high rpm´s (+110) and changing hand position to get used to the more challenging aeroposition, that puts extra stress on your hip flexors as this muscles ability to contract is decreased as you change the working way of this muscle as you reduce the origin and insertion.
When I hit +100 rpm for more than 30 seconds I start feeling loosing coordination and some of the auxillary musles, ie the tibialis anterior, fatigue. This proofs that my intermuscular coordination is not yet adapted to this way of working.
One of the often ignored components of strength is this intermuscular coordination that makes world class athletes make extremely complex movements look natural and makes us more fuel efficient and powerful as endurance athletes.
Keep working on that good effortless pedalling - imagine Lance Armstrong spinning +110 rpm´s in his aero position!!!