Thank you for your post and taking the time to outline your knowledge so concisely.
From what you have written, especially re: automation I would recommend the Logic 101 tutorial.
I was surprised at how much I learnt from it even though I train others in Logic. Of particular interest to you would be topics such as using busses, automation, MIDI editing and recording, using the other editing windows, screensets, channel strip settings, the environment and the mixing tricks - although there are so many workflow enhancements that I feel you'll also enjoy
From your description of using the plugins then I'd also recommend the Plugins Unplugged tutorial. Although this particular tutorial was written for the plugins in Logic 7 apart from a couple of minor differences (mainly aesthetically) Steve Horlick does an amazing job at explaining how all the parameters work within the plugins and does so with 'real world' examples.
In fact, both Steve and Martin are trainers of the highest quality because they are able to demystify in a few hours of video what can take a day or two to teach in a one-to-one environment.
Out of interest what kind of music do you make & how long have you been a Logic user?
Also, I'm not sure i understand this point:
[i]I cannot get rid of noise when embedded in audio when you want to keep the audio.
Are you refering to clicks/pops when cut regions sit next to eachother? The crossfade tool will be helpful for this. Or do you mean background sounds, e.g. noise from a computer fan behind a voice? Check out the denoiser plugin or SoundTrack Pro!
Let me know if you have any more questions.