I don't think the bus will be a problem, but do reserve when you arrive in Madrid. Go to the bus station and purchase your tickets.
There is a lot of labor unrest in Spain. The workers are feeling the pinch of austerity. I was in Leon during one of the last "huelga" marches. Stores closed so that they would not be vandalized by the marchers, but opened as soon as the march was over. I don't know if there will be any labor day marches in Pamplona, but it will be commerce as usual once the enthusiasm is over. Marchers need to eat, too!
The Albergue Jesus y Maria is mercurial. New management took over a year and one-half ago, and it is a less teutonic place. The policy is that you need to have walked in to get a bed. However, in October, they sold the person joining me a credential, and we got beds without fanfare. We had arrived together on the train, though I had been walking for weeks on other caminos. I suggest that you give it a try, and if turned away, go to a nearby hostal for a private room (or Casa Paderborn down by the river).