We rode through Nepal in May with no problems at all. We shipped the other way (Kathmandu to Bangkok). As long as you keep off the roads when there is a strike the maoist's wont bother you at all. There are daily riots in Kathmandu, its all a bit of a farce really. Each day the protestors gather on a certain road, the disturbacnce takes place, they get thrown into the back of a police truck, released later that day and the whole process kicks off again the next day. There is no trouble whatsoever on Thamel where you will probably stay.
Go to the Dynasty Hotel. There advertised rate is $60 a night, we got them down to $12. Its a very nice place and safe parking for the bike.
We have travelled from the UK and so far Nepal is the highlight of our trip. Ride across to Pokhara and then down to Chitwan if you get the chance.
You will have a great time.