Yes I've ended coexistence a couple of times. If you have the document on ending coexistence then I wouldn't follow it to the letter. I couldn't be bothered creating new data sources, ODBC's, etc. All you need to do to end co-existence is run the jobs indicated in the document. Then use the R98403 to copy all tables from the AS/400 - Common - PROD to to Control Tables - PROD. Then Remap the server and system OCM's.
Instead of the new datasource just use an existing one. I usually lock everyone out of the system and then use the R98403 to copy Busines Data - PROD and Control Tables - PROD over to CRP ot TEST (You need to lock the system to get a point in time snap shot over to the other location). You must use the R98403 to change the table formats over from DDS to SQL. Once this is done you can use AS/400 tools to copy the converted data libraries back to the production libraries.
Lemme know if you have any more questions.
Colin