Random missfire and transmission problem

1999 grand prix gtp with 145000 miles. It has 3.8L with a supercharger. About 40k miles ago I began having an intermittent cyclinder 3 missfire and rough idle. It would happen when the engine was cold or warm. It would be a very rough idle or very soft. It would go for days with no problem then I would have days where it felt like an earthquake. I took to the dealer and 1st they said induction service, then plugs and wires, then fuel injector #3 replacement. I fixed what they said and nothing worked. They told me my solenoids and compression were ok. I was too upset to go back there since. I've just learned to live with it for the past 2 years. Recently I've just had my transmission worked on under warranty repair from AAmco 9 months after they rebuilt it. After getting it back I'm still having problems. When I shift from R to D or vice versa it's very clunky and makes a noise. Also both wheels shake when I shift. This video is after I got it back http://www.youtube.com/watch?v=rVpTI4HkKIQ. After going back to Aamco they replaced my boost valve with an oem boost valve. I'm still having trouble which is http://www.youtube.com/watch?v=Hb0nU9BTy6o. Now Aamco says that the tranny is fine, that my problem is from my engine miss-fires. They say that my engine rpm is too high at 764rpm and that now my error code is p0300. Aamco did a scan and gave me the info that I included in the the picture file. They also say that my front right wheel bearing is bad. Also my valve rocker arm cover is leaking and I plan on replacing that. At 127k miles I had the MAF sensor replaced and the throttle body cleaned. Any ideas or advice about the missfires would be appreciated. Do you think my missfires could be causing the shifting problem? Thanks.