Your typical control system may consist of relays, contactors, motors, DC/AC supplies, transducers/transmitters, transformers etc, so understanding how these work shouldn't be hard based on the fact that you have your masters in EE. So having a formal education will indeed speed up the learning curve. Within my short time period of being in the automation field i realized that what truly matters is how you design your control system, you have to take the time to truly understand the correct way of designing a system, this i believe is critical, and as you will see you will get better in time, nothing beats out your time out in the field, because then you truly see how a machine really operates in the real world with real world problems.
How to become a master PLC programming?? well i don't think their is such a thing, as others have mentioned you are always learning, and although you can't really master the subject you can be good at it. Go over other programmers code, ask yourself why did they program it that way, having a PLC to practice on or a simulator will help.
Im a firm believer on teaching ones self, don't wait for others to teach you or you will be waiting a long time. Seriously their is so much wealth of information on this forum, the web, youtube, books, google, everything is their you just have to put in the time and research.
Don't ever look at ladder logic as coils and relays, but a set of instructions and functions that aid you achieve your goal. It is critical that you understand fully how these instructions work. Know how a PLC's scan time works, different manufacturers have different scan times so know the difference.
I would also add a programming language to your background if you already don't have one. Im not saying go attend another 4 years at your college to get a degree in computer engineering, im saying take time out of your day to pick up a programming language. The reason why i say this is because a lot of HMI applications out their have a lot of scripting capabilities, some even have full blown programming languages, like basic, VB, Jython etc. Visual basic is a good start.
Learn how to program in structured text, function blocks, sequential function charts, because you may be out in the field one day and if you limit your self to one plc programming language you don't want to be scratching your head trying to figure out what on earth is going on. Always be willing to learn.
Networking!!! ethernet IP, modbus, devicenet, control net, DH+, serial rs232, understand how these protocols work, how to wire them in a network correctly, this is also very important as you may realize out in the field in industrial application these are some of the methods through which devices communicate.
i have said all this and believe me i didn't even scratch the surface as to how much other stuff their is i did not mention.
Lastly don't be afraid , if you don't know something ask, it may seem like a lot, but once you start putting in the time, look at yourself a year from now and think back when you asked this question on the forum, you will be surprised by how much information you can get in a year.