Do you have a scanner? Can you download the trouble codes and post the code number and descriptions here? It would also be good to see the short term and long term fuel trims. Both at hot idle and after 30 seconds at 3,000 rpm.
The first thing you think of with rough running is vacuum leaks. You have replaced the vacuum lines and the problem is getting worse above 3,000 rpm. This is the opposite to what a vacuum leak does. They are worse at idle and go away at rev's.
How old are the spark plugs?
Is there any oil in the spark plug wells shorting the plugs to earth? Caused by old valve cover gaskets.
Have you replaced the HT leads to the plugs?
Could it be the expensive coil pack failing?
