Ok thanks everybody
A BIG thank you to Guzzisteve in particular for letting me know a possible spare is available if required. I don't think it will be required as the damage can be pretty easily rectified (I hope)
I'll post up what I finally do, ductape is a good idea but I still prefer a decent bung or an plastic patch. It was just through chance that I had to remove the airbox top and even then the hole was not that obvious. I had been cutting hose close to the box with the top off, so I was doing an inspection to make sure nothing had fallen in there (it hadn't) that led to the discovery
Then when trying to get the box out I discovered the second hole at the front.
Airbox and filter were clean, but as it just had a new filter installed by a PO there is good chance the box also had been cleaned out. The one at the rear particularly worried me as all the crap from the rear tyre would be thrown in there and into the airbox, albeit the holes are small.
I wonder what other "gems" I'll find along the way?