For searching, I sometimes use GrepWrap. It can exclude files and directories based on regular expressions (e.g. don’t search any directory starting with “Build” or “Tool”). It is a completely separate program that uses GNU grep. Search-engine it ™ :-).
For tagging, I use a version of the TagsJump plug-in for NPP that I have modified somewhat for my own needs. I recommend you try it out if you have not yet done so.