First off, let me say that I'm VERY happy with the quality of the engine kit, components, and assembly manual. However, just like any set of instructions, there are a few areas that needed further explanation. I put together a write up of my questions, Sonex's answers, and my comments as I went through assembly of the engine. Sonex is working on a revised manual, which will undoubtedly address some of these things, and probably more. Jeremy wanted me to mention that the new manual (Revision F) will be available free to any builder, even if you have an older manual. But, if you have the old-style manual, this might help you out.
My AeroVee Assembly Manual Comments (.doc)
AeroVee Kit (photo from Sonex)