Is it possible for you to capture a snip of HWMonitor when it slows and the post it when things are back to normal.
If your HDD is up around the 70 mark then that is way too hot, but it's interesting that after it has been off for a few hours that it boots up okay - which could also point to memory.
http://www.buildcomputers.net/hdd-temperature.htmlAudio and your GPU aren't in use in Safe Mode so it has to be a commonality to both those modes.
Next time it slows, shut it down and remove all sources of power and hold the power button in for ~30secs then see how it boots up.
After a few hours, the caps will also have drained as well as any cooling, so if it boots up okay after the cold boot then that would point to memory.