BMW Repair: Rough Idle......hopefully wont turn into broken car beyond my means to repair it! Ha Ha!, spark plug wires, centrifugal forces

Question
I have a 1988 325IX with 168,000 miles.  Some of the things I have done recently: new belts, water pump, fuel filter, thermostat, fuel regulator.

I started it up a couple of days ago and it would vibrate pretty badly.  When I gave it gas it would get worse as the clutch tried to engage then kind of smooth out but only because the centrifugal forces of the engine made it less noticeable.  I could only get 60 mph on the freeway for the 45 min ride home.  When I got home I parked it for 3 days till I could get it to my friend who works on BMW's.  We pulled the spark plug wires while the engine was on and it got worse when we pulled them except for numbers 5 and 6, that told us that they weren't working.  We shut the engine off, pulled all the spark plugs; 5 and 6 were covered in oil and gas, and replaced them with new ones.  (On a side note, I had previously installed the wrong ones even though I had pulled one out of my car, got the part number and looked it up.  They (AutoZone) said that Bosch didn't make that model any more but had issued one to replace that model so i put those ones in.  A lot of good that did.)  So after we got the new ones in we decided to drive it for a few days to see if the computer would change the amount of fuel going to the cylinders because it would have changed when those two spark plugs went out and was sending too much fuel to the cylinders.  After driving around for a few days and special trips on the freeway to give it a high rpm run for a good 40 minutes at a time, it still has that vibration at low rpm's.  It still happens at high rpm's but it's less noticeable. I pulled spark plug wires 5 and 6 to see if they werent' working, but the were cause the engine didn't like it when I pulled them.  Please help my figure this out!  I love this car and want to keep it till I'm 60 if i can.  I'm driving myself nuts trying to figure out how to make it run smoothly again! Any thought or ideas?  I would really appreciate your help and advice!!!!!!!!


-Begging for help in Utah!

Answer
Have you adjusted the valves?What was the fuel pressure? Why did you replace the regulator?Had you also replaced the timing belt?Just a few questions that would send one in the right direction.Also have you done a compression test?And finally how did the distributor cap and rotor look?Let me know