A good background article by Ben Anderson of Autosport on Honda's woe's. It includes an interview with Honda's Yusuke Hasegawa.
http://classicplus.autosport.com/pre...494.1448115426
In it Hasegawa basically says that the source of the problem with the new engine is when it moved from a single cylinder prototype to 6 cylinder. It was at this stage that vibrations first appeared that are the source of the reliability problems. It seems that the new V6 first ran on the dyno at about Christmas. It was only when the engine made it into the car did they realize how bad the problems were.
As this new V6 is very different from the old one there would not seem to be any chance of using last years engine to solve the problems, for example the crank is lower and it now has a turbo/generator set up similar to Mercedes.