Next time just make a backup copy of your game directory with GWX installed when it's stable and running. If you screw up next time, you won't have to re-download the game again.
Also, make sure to follow SH3Cmdr installation guidelines!
About "most realism possible", depends on what you mean by that, really. 'Cause you know, there's:
- "tactical realism" - fully manual targeting by means of getting all the targeting data yourself, speed, distance, AoB, etc. There are mods that add "Rings o' Confusion" or AoB calculators and other tools.
- "hardcore realism" - all of the "tactical" stuff above + manual navigation by the use of sextant and stars/sun (...and a useful Python script - search for "real navigation" here at subsim)
- "realism realism" - you know, as a captain you delegate most of the stuff and take care of the "high level" decisions and some of targeting... So.
I myself play on "tactical realism" level, where I like to calculate solutions on my own, using tools like "Rings o' Confusion" and stuff, and leave navigation to my officers. But maybe one day I'll try real navigation, as it sounds tempting. I imagine finally taking my boat there-and-back safely AND by means of manual navigation, and you know, finding actual way home... Sounds like doing something like this would be incredibly satisfying in the end. But I'm still way too set in my noobish ways.