Refer to the links for your first question.
Configuring the Transport Workflow (SAP Library - Software Logistics)
Workflow for Approving Change Requests - SAP Business Workflow - SAP Library
For this requirement you have to be thorough with the functional nodes, anything in addition or out of standard need to be brought forward and assessed for possibilities in standard system and then you can decide for ABAP intervention.
Yes, you have to gather information even after getting the BRD for example if your client is having group of companies and if there are minute legal changes for each company and if not covered in the BRD then this can escalate at later stages.
This depends on your landscape, in general there will be two dev clients and one of them will be the dev quality where you will be importing the CRs and do the unit testing and then release the CR for UATs to quality if found suitable then you can make a list of all approved scenarios and the same can be imported into PRD client during cut over activities.
Functional Specifications there is no standard format, but in general it should cover Requirement, Pre-requisites, Process steps, Process logic, error handling requirements, details of T. codes, screens, Information Types etc.
BR
Upen