Oldsmobile/Buick Repair: 1996 Park Avenue shaking running engine, vacuum leak, running kind

Question
I got this car since about 2 months and put a lot of work in it but it seems like it still needs more work :)
the car has 184K on it and I replaced the oil, fuel, transmission, air filters etc. plugs and wires, pcv valve and the last thing I did last weekend was to replace the fuel pump. I got it from the junk yard, the said it was the right one for a supercharged park avenue. the pump isn't making any noise anymore, but the car is still running kind of shaky. Mostly when just start it in the morning and start driving I can feel a shaking it seems to come from the engine. (No engine light is on) sometimes the shaking would become so bad that the needle on my speedometer would shake. that happens often when I hear the engine shifting into a lower gear going around 45 MPH and when I start to accelerate then up to like 60 MPH.
And my battery seems to be charged pretty high, the needle on the display almost touches the red area, but sometimes it's in the normal area (a little over half) and my cigarette assembly including the light above it stopped working. first it would need a long time to heat up no it started to work. the reason why I mention that is maybe it could something to do with the alternator? battery, and ignition system? misfire or something? the engine seems to run pretty loud and rough, but sounds ok in idle.
please help me with some ideas.
aah, and my supercharger is rattling, I'll probably need to  replace the bearings and the coupler in it.
Could a bad supercharger interfere with the harmonic balancer and that causing the engine to run rough?

thank you for taking your time to read.

Answer
Hello Robert,
First thing....check the oil in the supercharger. There is a oil level plug, and it takes a special oil from the dealer. real expensive oil.

Then test the fuel pressure, and make sure it is what that engine calls for.

Clean the egr valve. If it is dirty, and closes on some carbon, it will act like a vacuum leak, and make the engine run rough.
There are other possibilities, but those are easy to check.

And quite honestly....if I owned it, I might try some different oil in the supercharger than that expensive stuff.

Van