Question: I was wondering if anyone has a recommendation for a cheap, clean hotel in Mashhad. The famous non-smoking guesthouse is not an option.
Also I wanted to ask about the train from Yazd to Mashhad? Is it worth the time and effort or should I just catch a flight?

Answer: In Mashhad get close to the shrine and you will find a lot of good and cheap hotels. For more information check: http://www.uppersia.com/Iran-hotels/mashhad-hotels.html

If you have enough time (about 12 hours) the train is a good idea especially the night train otherwise fly for an hour to get there. http://www.uppersia.com/Iran-transport-services/iran-train-ticket-booking-service.html