Hi MYISSL
Some of these sound like well known and experienced problems. I have had the last 3 issues on my SL (all in my first year of ownership). Some comments below:
- centre speaker rattle. Seems to disappear upon firmly pressing down, but then returns shortly after?
This is most likely not the speaker at all but rather the dashboard and clips, which is why applying some pressure to it stops the creaking. I had to switch Lexus dealers because they wouldn't even discuss my options with me stating that Lexus don't cover creaks and rattles inside the cabin after X kms. Fixing this involves taking the whole dash off and putting it back on with revised clips and takes a while. The trouble is once you hear the rattle (my wife couldn't), it starts to really annoy you and you'll want it fixed. It took a whole day for Lexus to fix this.
- rattling/knocking noise upon start up. Has clean, full synthetic engine oil...
Search a bit more and you'll find some good explanations for what this could be. Mine did it more often when it was cold and I also got this fixed under the extended warranty. Something about "cam gears"?? There is a fair bit involved with this fix from what I understand so it will take a full day.
- rotten egg smell emitted from exhaust. Seems to make its way through the air conditioning system at traffic lights unless A/C is set to recycle.
Didn't fix this, just got used to it. Perhaps one day I'll install some after market mid pipes.
Good luck with your creaks, once you fix one you'll notice the next one and so on.