Firstly thanks for the replies!
OK, so I reseated the engine cover last night. Definately wasn't fitted right. No noise this morning, but it appears to only happen when it is cooler so early days as it was pretty warm here this morning.
Next things I'll check will be:
> Drivers foot well trim
> Windscreen water sensor
> Plast trim on front pillars (is there an airbag in there I should be worried about if I start prying off trim?)
I've bought some plastic trim tools and felt so I'm armed and ready!
I've got the rear deck creak/pop to move onto after this, and also just fixed an exhaust rattle (as per here.)
Will update you guys in a couple oe days (provided its cold enough in the mornings)