Well I examined my cable today and pulled it out of the casing. No issues at all and very smooth. I cleaned and degreased it and added a thin layer oil that I let dry before siding the casing back over. So for sure I know its not my cables. After the cleaning they are even better than before. As far as indexing and messing with the barrel adjuster there is no setting that will fix the current issue without causing another--this is even with super small incremental turns.
B-tension does not make a different even when fully loosened. My hangar is tool aligned but as mentioned by Andrew not necessarily derailleur aligned. Visually I cannot find any noticeable deviations from the plane of the cassette. Because of this I believe there is either 1) An issue with my pulley cage 2) To much play on the derailleur bolt or 3) A problem with the chain.
Maybe another useful bit of information is that sometimes I will get good shifts on my first 3-4 gears but it's more bad than good. I thoroughly cleaned my cassette and chain and checked for any play in the cassette. Visually I cannot find anything wrong with it and it feels very solid too. For the heck of it I'm going to test out a new chain and see if it makes a difference. When I get time I'll mess with the hangar to and bend it very lightly in or out to see possibly the derailleur itself just isn't in the same plane.