mmm Jiminy had a journal from C.O.? even in the early begining of KH II we saw the last part of it! "THANK NAMINE" so who nkoes? XDD
CoM Journal = KH1 Journal.
At the end of KH2, Jiminy had two journals.
The KH1 one which got erased during CoM and only had the message 'Thank Nami' on the first page, and the KH2 one.
Upon looking through the KH1 at the back of the book was the message 'We must return to free them from their torment".
Since this was the journal for KH1 THAT is why they go back to KH1 time.
Anyways, the CU (Coded Unknown) doesn't have to be from KH1 or CoM. He most likely is from outside of the data world as well as being able to go inside of it (due to him being in a scene with Mickey, Donald and Goofy at DC).
He could be anyone. And, just because an Org member died, doesnt mean they didnt come back as a complete being. There's also the chance it isnt even an org member at all.
Most likely though, it is Xehanort as a complete being.