Hi,
I don't cut and paste. I'll give you 8 hours of my time spread out over a week, email preferably then you can compose your thoughts, do some research and come back to me with more informed questions. Skype would be a poor return on your investment.
I've been doing LAMP from bare metal installs when it was a hobbyist project to billion hit websites for the last 15 years. I have my own personal opinions on what is best, some may not gel with "best practice" (recently I set up a db to theoretically use 150% of the available memory because it would never reach that level but gave performance enhancements at the indexing level) but I'll give you all the options and if I don't know something then I'll come straight out with it and find out the information fast as my searches would be based on a massive store of seemingly disparate information gleaned from many sources.
I've seen companies paying out $29 dollars a month for four years for software raid that could have been set up by an administrator for $80, recently someone with the bright idea of running 6 cloud servers for redundancy but not calculating the cost of an administrator to keep the software up to date ($250 per month per server), a company that let $4 per item on 4000 orders walk out of the bank as they forgot to check that their invoices had the shipping added on, and another one that let £1500 worth of goods get sent fro the warehouse every two weeks to the russian mob because they said they'd send a cheque in and the system never had a "payment cleared" button. An invoicing system that changed address and so was declared "invalid" by the tax man and cost them £6,000 per day for a forensic accountant. Been employed to find SQL bombs programmed to delete entire websites by paranoid programers who thought it added to their job security.
I work on "the edge", the area where I'm employed to sort out mess caused by poor programming and structure, where people have gone for the cheapest option. Strangely I'm best known for my open source work on phpMyAdmin, fpdf, ZenCart and Drupal but get tracked down by multinationals to do "off forum" work when things just don't seem to be working. I would say this, "best practices are not built on success stories, they are built on learning and not repeating the mistakes made by others".
I'm an arrogant sod, but I will gladly share my knowledge, their is one proviso and so far the project posting has proved true, you must be willing to admit what you don't know, 90% of the businesses that I've seen go under were caused by someone over estimating their abilities. As above I feel no shame in admitting a lack of knowledge, I pride myself on being an old dog continually learning new tricks and I expect the same courtesy.
Philip.