Cat,
I finished the Transam August 11th. Started in Florence Oregon June 2. I was able to find motels in the $40 to $50 range quite often using the ones listed on the ACA maps. If you want to keep a reasonable budget, try to camp when the weather is good. There are private RV park/campgrounds that usually have grassy tent sites and shower/laundry facilities, state parks, and several small communities allowed camping in their city parks for the cross country cyclist. I found all the camping I did to be safe and was never bothered by anyone. You'll also meet other riders and will have the opportunity to ride and camp together. Yellowstone Park was the only place I had any issues with a place to stay. I was riding with a couple guys I met earlier and was figuring on staying in a hiker/biker site only to find out that is wasnt open yet. The ACA map read the camp area opened mid June. We were there June 18 and it was still closed. A park employee invited us to camp on his site at a employee RV park. There are also a few hostels along the way. I have a journal on the crazyguyonabike.com website. Log on to the site, click the link for journals, then enter Hobodog in the search journals box. You'll see Transamerica trail 2012. If you would like, I can make you a list of motels, campgrounds, and Hostels that I found comfortable.
Mark