CheckPilot...
"$3.50 to $4.00 per square foot for the material. I charge by the hour on these kinds of jobs"

I think it is less than $1.00 / sq. ft. for material. Around here, you can get about $1.50-$2.00 sq. ft. for large volume builders, and about $2.00-2.50 for small, custom builders, excluding options.

BTW,

I agree you can't bid by sq. ft. Unit pricing is the only way to go. Although, afterward you can calculate the sq. ft. costs