We're leaving on the same route in 2012, starting the first few days of May. I have budgeted $4,200. Much of the first half of our trip (through Kansas at least) includes many free places to camp/stay. Places such as churches, fire stations, city parks, and Warm Showers hosts. We're planning motel stays probably once a week, but there is a minimum of two of us to share in lodging costs. We're cooking a lot of dinners, the majority of our lunches are planned from our panniers. Only breakfasts will be eaten out (cafes and such) most mornings.
I've already ridden from Yorktown, VA to Carbondale, IL, so I'm way ahead of the game concerning what to expect to the Mississippi. After that it's all new riding terrain for me. We're riding to Florence, and then turning south to San Francisco along the coast. My budget has to include an Amtrak ticket back to Illinois.
I plan to be as frugal as possible. Last trip I was managing pretty well in that respect...until my bike broke necessitating a new bike...and a busted budget. It's built back up now and I'm ready to go again, but my ride mates won't be ready until 2012.
If you haven't already, start reading some of the TransAm journals at
www.crazyguyonabike.com you should. Many of the stops I have used and those I plan to use, others have written about in their journals. Another source is the TransAm Trail map sets from Adventure Cycling Association.
http://www.adventurecycling.org/routes/index.cfm They list many, many places to camp, and over night stay on their maps.