I've experimented with the short housing going into the rear D to no avail and the rear D is brand new and perfectly clean. a I'm curious about Losi's suggestion of checking to make sure the right side of the chain is facing out. I'd imagine that would only be an issue for a chain and cassette that have worn together but I could be wrong. Both the chain and cassette are brand new in my case.
regarding flushing the shifters, I did spray a fair amount of wd-40 into them when I noticed the previous owner appears to have used a lubricant of too-high viscocity.
The issue with that was the pin would engage/disengage and the shifter would not click and the shifters would opperate smoothly but slowly. Now the action is quicker and it clicks every time so I'm guessing that means it's taking in/letting out enough cable.
All of your insight and Ideas are great so far. Even if you're not pro mechanics, sometimes it helps to have a different brain think about it.