Designed and manufactured by Northrop, later Northrop Grumman, the cost of each aircraft averaged US$737 million (in 1997 dollars). Total procurement costs averaged $929 million per aircraft, which includes spare parts, equipment, retrofitting, and software support.
Northrop Grumman B-2 Spirit - Wikipedia
https://en.wikipedia.org/wiki/Northrop_Grumman_B-2_Spirit
Designed and manufactured by Northrop, later Northrop Grumman, the cost of each aircraft averaged US$737 million (in 1997 dollars). Total procurement costs averaged $929 million per aircraft, which includes spare parts, equipment, retrofitting, and software support.
You stopped reading too soon. The source you quoted also says:
"The total program cost including development, engineering and testing, averaged $2.1 billion per aircraft in 1997."
From what I've read the $4B quoted for the AF1 program is total program cost.