It's not quite clear what you are after, but I'll take a stab at it. This would join the "starts" to the "ends" and allow for any "adjustments" in between. From here you can do whatever math you might desire.

select * from

#InvLogData TheSs

Inner join

#InvLogData TheEs on TheSs.Manifest_Id = TheEs.Manifest_Id and TheEs.Doc_Type = 'E'

LEFT OUTER JOIN

#InvLogData TheAs on TheSs.Manifest_Id = TheAs.Manifest_Id and TheAs.Doc_Type = 'A'

where TheSs.Doc_Type = 'S'