Thanks heaps, I'm always interested in learning more about the history of the game and especially Collingwood.The article of the Referee is correct in at least some details.
A combined junior side did play Carlton in 1891(cf the Australasian of 14 April 1891
http://nla.gov.au/nla.news-article140171956
which they won easily
http://nla.gov.au/nla.news-article8634581
and Clifton is reported to have disbanded at lest by 1893 and a new collingwood juniors club created
http://nla.gov.au/nla.news-article59755762
And again a merger of sorts between Britannia and Clifton is inferred in this 1917 article:
http://nla.gov.au/nla.news-article120295974
And here again in 1916:
http://nla.gov.au/nla.news-article121174237
These only talk about Britannia successfully applying to join the VFA as Collingwood in 1891
http://trove.nla.gov.au/ndp/del/article/8617318
http://trove.nla.gov.au/ndp/del/article/193413388
however the book CFC 1892-1948 contains an interview with E. Wilson who was the club's first Secretary. In terms of players "We used a few from the old Britannia, but we got others from Preston, Clifton Hill United (Mr John Wren... was a noted wing player in that team and we asked him to play...)", so perhaps it was more in terms of players?
Piecing it together, from what I can gather:
1891 - Britannia application | Collingwood admitted to VFA
1892 - Britannia disbanded | Colllingwood VFA with players from Britannia, Clifton + others | Clifton juniors
1893 - Collingwood VFA | Clifton disbanded | Collingwood Juniors with players from Clifton + others in VJFA
I know Collingwood Juniors acted as a feeder club for Collingwood, eg your link http://nla.gov.au/nla.news-article59755762 refers to Halewood, who I assume to be http://forever.collingwoodfc.com.au/players/frank-hailwood/
A guess, but Eastham could also be Eastman who was later president of Collingwood District, and for a time our reserves B+F was named after.
1904 March - CJFC presented VJFA runners up caps http://trove.nla.gov.au/ndp/del/article/197234312
1904 April - Collingwood Juniors in North Suburan Football Association (3rd rate clubs north of the Yarra) http://trove.nla.gov.au/ndp/del/article/67428827
1904 - Fitzroy District admitted to MJFA http://www.vafa.com.au/history/history-vafa/
1905 - Collingwood Juniors disbanded http://trove.nla.gov.au/ndp/del/article/73254774
1906 - Fitzroy District name changed to Collingwood Districts and played at Victoria Park
Correct me if I'm wrong, but from what I gather the VJFA was the VFA reserves while the MJFA acted as the VFL reserves. Complete guess work, but perhaps the introduction of Fitzroy District lead to Collingwood Juniors stepping down a level and ultimately disbanding, which in turn allowed for Fitzroy District change name and move to Victoria Park?