Joel,
From memory, all your numbers work out. The '69 SS427 used 390 hp engines whereas the Caprices and base Impalas (generally) used the 335 hp version though exceptions have been found and both ways I might add. I personally have a '69 335 hp 427 that was pulled from a '69 SS in 1979 so it can happen. I also have the POP for that car. Your trans and rear numbers also sound correct.
The differences between a '69 standard 427 and an SS427 are very few. Basically emblems which are all easily added and that is why it is so easy to fake a '69. However, with your documentation, that should be a non issue.
If I understood your last question correctly, there were 2455 '69 SS427's built. I know of no honest figures that determine how many of those were auto compared to manual though the automatic was obviously much more common.
Also, check out
www.impalass427.com if you haven't already.
Rick