I read as much of the NASA report to the NHTSA as I could understand. NASA did NOT rule out an electrical or mechanical problem with the Toyotas. They did state that the ONE car they studied didn't exhibit any electrical or mechanical problems that could cause unintended acceleration.
Face it, cars are extremely complex and as with any sufficiently complex systems, unexpected and unintended emergent behaviors will occur. The reason automatics have the brake interlock system was because of a problem in some Audi's in the late 80s jumping when put into gear.