I get the feeling that the delay with the fifth kit and it going through such a long tweaking probably dealt with the CPU since there was a small performance boost. There were enough problems arising in the 4th kit pointing to the CPU to not think it was ignored during that roughly six month tweak period.
Remember a while back wsippel found out that the latest version of the compiler for the Wii U broke compatibility with older libraries? As I pointed out at the time, this could happen if IBM and Nintendo removed support for some instructions while trimming the transistor count for the final silicon. As the V5 dev-kits apparently started shipping to devs shortly after with production hardware, it does seem to be the case that there's a difference in the CPU compared to previous dev-kits. It's likely to be quite minor at this stage, but it's possible that they were working to get the compiler working better with the new CPUs, or even that the reduction in transistor count allowed them to hit higher clock speeds than they were expecting before.