as for #1,i am still stock. im pretty boring when it comes to kernels and other mods,so id be interested in hearing others experience with this also.
to answer #2,its very likely that wifi issues are due to a module/kernel mismatch. reflashing a rom,or restoring a nandroid generaly will repair such mismatches. bluetooth,im not sure... but it may be possible to break it as well with mismatches.
to answer #3,if you were s on,then you couldnt make changes to /system while booted,youd need to make them in recovery. while s off,all write protections should be gone,allowing you to change things in /system as you wish(delete bloat,etc)