Are guest houses basically safe and clean?

In Tibet, 'hotel' is usually used as a hifalutin term to denote a superior [read more expensive] establishment; but not always. GHs are more of a family operation in most places, often a good thing.

Lhasa has very good standards in the well-established hotels.

Standards of cleanliness is a highly personal matter, of course. Even relatively fancy joints often shock in the toilet department; outside high priced places, a hole in a floor is good; sometimes you have to wander behind a wall in the freezing wind. This is in the countryside.
Rooms are almost always OK, if you don;t look too hard at say, pillows and bedding. I carry a ground sheet and old sleeping bag - works well. You come across pillows filled with sand, work well once you get your head indent worked out.

Mugging, that familiar American expression..one sees very little violence in Tibet; women travellers report few incidences with men, so its a safer place than your home turf! Tibetans are tolerant and easy-going folks, lovely people really; it is a real culture shock when one returns to what passes for 'civilisation'. Nearest I got to be 'mugged' was an encounter with two PSB guys in Ali, everyone else, including Chinese soldiers were very friendly.

Budget travellers find it far more expensive than say, India or Pakistan, but way cheaper than most other places. I hope you both like it...

Thank you very much, Philip.
--Morty