I predict that you will use other mods. Compatible STFU's and no autonomy mods are available from Twoftmama @
http://www.the-isz.com/theisz/ - unfortunately this website requires you to register these days but it is worth it.
As far as best method you've proably already figured this out, but;
- patch, patch and patch again
- make sure the framework is installed properly
- 3 booter isn't really necessary for the game anymore, but it is how the framelimiter loads
- get the frame limiter
- goes without saying but get AWESOME
- decrapify your mods
- where possible use combined packages