Ok, firstly let's consider this may be being caused by water ingress or damp. You're not the only one who's suffering from these symptoms right now..
So, bit of a long shot, but have you checked all your earthing points for a good connection/corrosion?
And have you checked your ECU for signs of ingress/corrosion? As well as the fuse/relay box in the engine bay?
Have you checked all exposed electrical plugs in the engine bay that could have taken in water from a deep puddle splash?
Other ideas..
When was your cambelt last done? If it's worn, it could be slipping teeth every so often - hence running good, then running poor.
When were the valve clearances last done?
Have you checked the tension on the cambelt? The auto-tensioner could be on it's last legs. Or if it's got a manual tensioner fitted, maybe it needs adjusting.
Could it be your O2/Lambda sensor is knackered, & confusing the computer?
Or, finally, is your catalytic converter blocked perhaps??
