So after some further investigation it turns out that one of the chainstays is in fact higher than the other. Turns out they were welded on the BB about 1mm off. Rookie mistake. Of course I figured that out after I was trying to align the stays myself and ended up denting the under side of the DT. Yet another rookie mistake.
You live and learn I suppose and I def won't be make those mistakes again.
Time to order some more tubing I guess.
Thanks for all the help.
Brandon