Optical Element Alignment After Disassembly

I have a Canon EF 70-200 2.8L IS USM. The MF ring doesn't work but the AF works most of the time. Sometimes the AF seems to "get lost" and doesn't want to focus, but will eventually start working again. My guess is that the encoder disk is dirty or scratched, affecting the AF. The MF ring is probably slipping. I am thinking about taking the lens apart in an attempt to see what's going on. What is holding me back is that I have read that the optical elements must be realigned following any disassembly and it is not exactly DIY friendly. I am interested in opinions from people who have done similar disassembly/repairs like this, and what their outcomes were.