Unless you happen to be extremely lucky, a manual installation probably won't give you a stable game.I tried going through each mod separately in Big World but half of the descriptions are completely wrong and are for a totally different mod. Also, editing the .bat file is like staring at gibberish, so I guess I'll have to manually go through and install things the way I want them. Oh well.
You are facing the same issue I had. I recommend persevering with the Big World Setup as its installation routine is a lot better than manually going through each mod and working out which components will affect others (I tried this as I wanted extra kits and different options for some tweaks, took 12+ hours and I had nothing to show for it except experience
![:P](http://www.shsforums.net/public/style_emoticons/default/tongue.gif)
Anyway my point is that you will gain the customization you desire and (most of) the stability needed for enjoyment by selectively editing the Big World Install.bat after selecting and extracting the mods using the BWS program. I made a post a few hours ago detailing some selective editing I attempted (which worked!) so that might help you.
I'd get a good Text/Code editing program like Notepad2 or Notepad++ as they have very handy syntax highlighting, and don't be afraid of being confused for the first few half-hours you stare at the batch file trying to puzzle it out. Once puzzled out it's very logical in what it does.