It is mostly stable, when playing RE0, but if I change scenes in a room sometimes there will be a huge dip in FPS, to where it hangs for a few seconds. Most of the time its fine, but every so often it will do this to the point the game is unplayable. Is there a setting I can uncheck or check that will limit huge frame drops to a minimum?
A "limit huge frame drops to a minimum" checkbox would be wonderful, but it's impossible to implement without actual magic. There may be some option that reduces them, but it can't use magic, thus it has to have some logical significance in the equation and may not be foolproof.
Humorous musings aside, the usual causes of this are shader cache generation and disc loads. Both can be mitigated by putting the Dolphin folder and the game itself onto an SSD or RAMdisk.
You may also want to try overclocking further, though I don't know how useful that would be here as it's unlikely that you're running into a CPU bottleneck.