I have done a similar route back in 2007.
Andorra is a nice place to stay. Was overpriced then but the whole city was under construction, with huge new hotels to appear in every corner. So, i belive that you will find something cheap. Due the tax free there are tones of tourists visiting this small country, so i will suggest to book in advance. Andorra la Vella is a modern city, not bad, but nothing special.
On pyrenees, we stayed for 2 nights on Eaux-Bonnes, a small town on the French side of pyrenees. There was only one hotel in the town, but there was availability. So i believe that you will find accommodation on pyrenees easily.
Borders was really croudy. It was a huge car line when we entered from France, but we bypassed with no problem. Another huge line was on our way out of the country. We bypassed again and had a typical border check control. I have heard that they check sometimes motorcycles cause lots of bikers go to the famous tax free biker shops for really cheap equipment.
You can check some photos from my trip here:http://motoadventures.wordpress.com/200 ... -pyrenees/
Hope i helped, if you need anything else just ask