Hi
Charles Robert Wheeler is not a particularly common combination on FreeBMD's transcription of the civil registration index. Coverage charts are here.
http://freebmd.rootsweb.com/progress.shtmlThis is a birth registration in the right place at the right time
Births Jun 1863 WHEELER Charles Robert Cheltenham 6a 387
and other than the census already mentioned there doesn't seem another sighting for that particular birth on censuses, or marriage or death registrations, so if it isn't him then this Charles Robert Wheeler would also have seemed to have disappeared. Given that the father of this Charles Robert Wheeler may be Captain Johnson's manservant on the 1861 census that does make a connection to this birth registration.
1881 census RG11 196 folio 20
29 Frederick Street St Pancras, London
Charles R. Wheeler 18 Boarder Midshipman Cheltenham, Gloucestershire
There is a Robert Charles Wheeler birth registered Cheltenham in 1865 but he can be found on the 1871 census in Cheltenham.
Is it possible there are other records for the Thames Nautical Training College that might include Charles Robert Wheeler and give further information?
http://www.nmm.ac.uk/collections/archive/catalogue/record.cfm?ID=WORThere is also a British Historical Society of Portugal.
http://www.bhsportugal.org/It does seem to have published on The British College in Lisbon
http://books.google.co.uk/books?id=VclMOAAACAAJ&dq=%22british+college+lisbon%22&lr=&as_drrb_is=q&as_minm_is=0&as_miny_is=&as_maxm_is=0&as_maxy_is=&num=100&as_brr=0&cd=2as well as on the British Cemetery in Lisbon. They may be able to help as well.
Have you researched Captain Johnson's family to see whether he did in fact have a sibling called Jane?
Regards
Valda