All except TREX configuration should be possible to transport as requests (workbench or customization). Basis can do the TREX configuration in the target system. If workflow task agent assignments are used, for example marking one or more tasks as General, those might have to be done in the target system also. You can transport changes in table T77S0 as well, use the menu entry Transport while in Change mode in transaction SM30. If the Switch Framework is used, relevant switches need to be activated in the target system as well. It sounds like not all changes were documented so you don't exactly know which changes to transport or adapt manually in the target system. You should go back to the persons involved in the implementation and make sure the entire implementation is documented so that you can have a succesfull go-live.
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