ok here it is a week later and I now have the header back on and have replaced the plugs and cables since I was right there and couldn't remeber the last time I did them.
Anyways it has been running fine up to this morning, on my way to work I got off the freeway and as I took off it began to sputter just like it was doing when the manifold was on it.
I have checked all my fluids and everything is good other than needing an oil change, the fuel filter is new and almost all of my vacum hoses have been replaced. And I went back over them a few days later just to make sure they are all tight.
Please help I do not know what to do at this point or what to even look at.
Thanks