Hi Grandfer - the Mk3's were built as Mk2s at Philly then transferred to Shrieveport where they had the new cockpit and associated systems etc installed. Of course some factory testing and customer testing was done there, as well as further testing at RWTS Boscombe. The "combined" test team did much to see how the system worked at a crew level and from a pure technical performance perspective.
However, what is good enough for post build acceptance as "safe" and to design is not neccessairily acceptable when an analysis of the design and its software is done against different (and sometimes more demanding standards) - which should have been understood and contracted for as part of the requirement in the first place. More to the point, any safety assessment has to be based on detailed data - which in the Mk3's software case was not forthcoming to the standards and extent required, not only as routine clearance process for such software driven cockpits but also for a UK Military Release in the demanding specialist role the ac was due to fly in. It therefore (rightly or wrongly depending on where you stand in this argument) was deemed unsafe for such a role.
Cheers