What you need to do is Full Outer Joins instead of Left Outer Joins. Join on Doc ID and Row Number.

SELECT COALESCE(dbo.GR.DocNum, dbo.GE.DocNum, dbo.Ref.DocNum) AS DocNum,

GR,

dbo.GR.Seq AS GR_Seq,

GE,

dbo.GE.Seq AS GE_Seq,

Ref,

dbo.Ref.Seq AS Ref_Seq

FROM dbo.GR

FULL OUTER JOIN dbo.GE

ON dbo.GR.DocNum = dbo.GE.DocNum

AND dbo.GR.Seq = dbo.GE.Seq

FULL OUTER JOIN dbo.Ref

ON dbo.GE.DocNum = dbo.Ref.DocNum

AND dbo.GE.Seq = dbo.Ref.Seq

OR dbo.GR.DocNum = dbo.Ref.DocNum

AND dbo.GR.Seq = dbo.Ref.Seq;