I used the manual here: http://www.rinnaisales.co.nz/tradesmart/rinnai2/pdfs/installations/190.pdf
I disassembled the pilot burner and injector.
I removed the thumscrew and the pilot shield and then unscrewed the two screws which held on the pilot shield mounting bracket.
I then removed the retaining assembly screw.
I then lifted off the pilot burner and blew that out, and then unscrewed the injector on which the pilot burner stood (using TWO spanners so as not to damage the pipe).
The injector inside was almost blocked with a sort of black charcoal membrane, so I cleaned that out with a cotton bud and put it all back together.
Now my pilot light covers the thermocouple when properly lit!
Sam, December 2009