Well, the carb rebuild went well. However it did not affect the motors performance that much. At first when it was cold and the choke was full closed it idled really well and I initially though that I had solved the problem. However as it warmed up it became apparent that I could only open the choke up(manually, because the choke assembly is still broken)only a tiny bit. Then the engine began to run kind of rough and did it's intermittent growling or shaking of some sort. Here are some of the things I noticed/ideas:

1. It seems to run fine cold and gets worse when it is warm.
2. The mixture needle wasn't in horrible shape but it was visible that it had been turned in too hard and therefore was mishapen.
3. I was able to turn the mixture screw all the way in till it was seated but engine would still run.
4.The EGR is now cleaned out and apparently operating (engine dies when vacuum is applied).
5.Choke can only be opened a little bit which seems to indicate that it is starved for fuel and getting to much air.

If you can think of anything that fits the bill, please let me know.