I suggest learning how to make items and behaviors, as they're basic scripts and make good easy hints to how the server works. For most endeavors in private servers it's more being able to toy around with the current engine setup by familiarity rather than superior knowledge in C#. (As for things like game restructuring, that just requires experience in coding and networking in general)
MSDN (microsoft developer network) is a very good source for answering any general questions and defining things in c#.
In terms of your code environment, I suggest the following tools/IDE's:
Visual Studio 2015 Community Edition - editing the server
XAMPP - database and webserver tools, far simpler and better than MySQL Workbench
IntelliJ IDEA Ultimate + Flex SDK 4.6 - editing an AS3 client source
RABCDASM - editing a client source in ABC
JPEXS Flash Decompiler - for all your client decompiling needs
paint.net - a very good free image editor with tools great for entry-level graphics/spriting