The book recommendations are great. "Mastery", though, comes only from practicing your craft. If you want to learn PHP, you need to build many sites, with PHP (and HTML, CSS, Javascript, MySQL, etc.).
To have confidence that you can build a secure online web store, well, you need to build one. Maybe you can find a company that will pay you to learn. Maybe you will find a colleague to mentor you through it. Or maybe you'll have to dig into books, multiple web sites, and some poorly written "integration guide" from a payment authorization provider. My first time through I was nervous. The second time it went a little quicker. And the third time I felt confident enough to estimate how long it would take.
I'm not trying to be difficult or flip. I just feel that "learn by doing" may be the only way to learn much of this stuff.
