Well, experience goes a long way.
After having built software in different languages for different targets on different systems a few times, you start recognizing patterns.
One of the strategies I use to become comfortable with new environments is to build a piece of software (usually a prototype) using only the core language, standard library and maybe one or two 'mature' pieces of third-party library code.
This takes a bit of time and I usually end up with a codebase that is a bit crufty (especially when I'm learning the language as I go). However, this usually gets me to the prototype stage with a lot of newly acquired knowledge about performance of the language, best-practices, etc. As well as a lot of testing code.
After that I'll start looking into third-party libraries and start factoring out my own code with third-party libs where appropriate.
For Java, for example, I've found that a lot of the language helper/util code I write can be replaced with code from org.apache.commons.
For interacting with crufty stuff like webservices in all their non-standard glory, I usually build a few classes in Ruby with breakpoints so I can interactively analyze and poke at them. Much, much faster than going through the 'change code'-save-recompile-run cycle with breakpoints in C# and Java.
When dealing with loads of XML config files, I'll quickly do a git init and also keep all the files open in vim buffers. (Vim and Emacs are excellent tools for working your way through XML junk). Then I'll put print (or equivalent) statements in the code so I can run the app from the command line and filter the output through grep or even some custom scripts that'll filter the output for me and provide some basic analysis or correlation points.
The list goes on and on.
You have to realize that apart from the code that operates solely within your codebase (and not even then), you are always dealing with third-party code. The OS, compiler, the VM, the windowing routines, the threading model, etc.
As you go on you have to learn techniques to handle this. And one of the first things you already seem to have learned is that you should never be quick to voluntarily add to the pile of third-party software you're already dealing with.
And that 10x programmer working opposite you who generates mod_rewrite configs like there's no tomorrow? Yeah, that person spent about 3 days getting to the bottom of that engine and testing the hell out of various configs a few years ago. There's not much of a short-cut for these kind of things.