Just a very quick update: things are slowly evolving, so DON'T PANIC.
Some more words about what has happened recently: I had some trouble with my Amiga, turned out as a PSU problem. Luckily it is already fixed with a "new" case for the poor girl.
I am fighting with the rather chaotic E-UAE sources, so I made a few steps to make it easier to edit the whole project: I managed to put together a cross-compiling environment from Windows. *booo-booo*
Compiling is much faster on the muscle x86 processor (*booo-booo*) and there are some advanced tools to do some heavy lifting when it comes to source code editing. I must also admit that since I use source version control at work, I barely can go on without it.
With the help of Cygwin, Eclipse CDT, TortoiseSVN, VisualSVN Server, FileZilla Server and a simple script on the Amiga side I was able to assemble a semi-automatic build and test deployment environment.
Thanks to Zerohero for the detailed cross-compiling setup description.