It could be ignition or fuel given the brief description of the symptoms:
When the idle speed goes up and down does it continue firing on both cylinders but just rev higher / lower? Or does it obviously run onto one one cylinder?
If both are still firing then I'd say there's a fuel problem, if it's cutting onto one then it's as likely to be ignition.
Given the rain I'd normally say ignition, but the fact that the garage had to clear out the fuel system means there *might* be something letting water into the fuel, which, after a few days settling out could cause the odd running you describe.
BUT, it's probably easier and cheaper to check the ignition first.
First option - drown the HT coils, HT leads, plug caps etc in WD40. If this helps in the wet then it's probably an ignition problem (but still not certain).
Make sure the HT leads are routed away from - and certainly not touching - anything metal. Make sure they're not chaffed or cracked.
Take the HT caps off the ends and check that the HT lead conductor is in decent nick. If not, cut the lead back a bit to find some good conductor.
Probably worth replacing the HT caps - they don't cost much for one of those.
So, try that, and tell us if it's cutting onto 1 or not, and we'll go from there.
arrrf.