I've managed to stumble along a little further with this branch after looking at the Littleport 1861 Census.
On it, was
Robert Cole, 23, Ag Lab, b.Ely
Caroline Cole, 25, wife, b. Suffolk
Backthen?Elizabeth Howlett, 5, stepdaughter, b. Littleport.
Now these three appeared as expected, except that the Cole name is really COE. Robert COE was Caroline's second husband after Thomas Howlett died only a short while after their marriage in 1855 at Mildenhall.
There was no sign of the WOODS family or any other HOWLETTs apart from a widowed servant, Lydia Howlett, a 40yr old housekeeper born in New Buckenham, Norfolk.
Still not really any further forward, i decided to do a worthwhile search again using Google (if you've never searched Google by putting an ancestor's name in, it is worthwhile!) and this gave me the site belonging to Albert Browne
http://albert.browne.me.uk and this led me to an Elizabeth Howlett born in 1835, daughter of John Howlett. Elizabeth's place of birth is noted as Wymondham, Norfolk... which matched the information given to me by the 1851 census of Mildenhall.
I scrolled a bit further down, noting that Elizabeth ("Betsy") married George Gipp at Ely Holy Trinity in 1854 and that they had 13 known children in Mildenhall. At the foot of the page was the evidence i wanted - the witnesses to Elizabeth and George's marriage...
Thomas (x) Howlett and Caroline (x) Clark.
This therefore accounts for the disappearance of Thomas' sister Elizabeth Howlett as she became Elizabeth Gipp. I am still yet to account for their parents and also for Caroline Clark's family.
Perhaps looking at the Mildenhall census for 1861 will provide me with the information i need as the COE family noted above were living at Mildenhall Road, Littleport, which must be on the borders of the county.