Using Lean methodology for Software development is a great approach, but implementing it with cards and whiteboards we've found a bit hopeless. To do it right, an integrated system that manages priorities and processes is needed that is virtually transparent in its ease of use. That's why we're making (shameless plug) StreamFocus.
The time we spent moving paper around to implement lean outweighed the benefits (One issue also was a team member in Europe, but that was not the major problem with using analog methods). Once we went to a program driven database system, we immediately started realizing large productivity gains. We're at about 35% higher efficiency with far better quality now, and hope to hit the 50% mark once the system is complete in the next few weeks.