The service manual specifically calls out to turn the crankshaft counterclockwise. Doing otherwise may or may not harm something. But there must be a reason Honda specifically calls it out. There are no cautions or anything against clockwise, but personally I'd sleep better doing it per the manual if it were my bike.

 

If the CCT is automatically tensioning, I'd be worried about turning it backwards....

 

There is a thread on here to do the CCT swap without removing the valve covers. As you say, TDC on compression is what you must have, not exhaust.

Thie trick is to remove a valve cover bolt on the front cylinder to enable you to see the cam lobe, and therefore determine correct piston position. Then the rear is simply a crank rotation a certain number of degrees. I have done this a couple of times and it works well, and is easy to do.

Do a search for the thread, and you will be home and hosed as they say!