Well I believe I have solved the problem, The issue stemmed from 2 things as I see it. First being the top pulley, And the cassette. I had 2 bottom pullies in the cage, luckily I had a top lying around. So once I got that fitted the chain skip seemed to stop, I checked the indexing without the chain and everything seemed to line up. Untill the Lagest 2 cogs. Once there I could no longer get clearance and the derailleur would get hung up on a cog. I was like a 12-32. I dont think the derailleur could hangle the big jump in the last 2 cogs. I had an old hg cassette and cleaned it up. threw it on also. Threw on a 8 speed chain. And viola. Well it still gets hung up on the last 2 cogs but I dont really plan on using them.
Thanks for the help