For question #1, I'd recommend a Consumers' Report print out for around $20. The report lists everything available, the MSRP, and the invoice price. That amount of knowledge puts you in a strong position. Also, remember that invoice price already includes a hidden 5% dealer profit.
For the other questions, I defer to those with deeper knowledge.
You can go to the Lexus site and do a "build you own" to come up with a option list and pricing. If you can nail down the options you want, you can shop the price with your local dealers and the internet.