Looping is very slow on large data set

Please try this:

CREATE TABLE #Final ( RwNum INT PRIMARY KEY, JobSource NVARCHAR(100) , RuleName NVARCHAR(100) ,PackageType NVARCHAR(100) )
INSERT #Final
        ( RwNum ,
          JobSource ,
          RuleName ,
          PackageType
        )
VALUES  ( 1 , N'Presubmission' , N'GameRating' , N'Xap'  ), ( 2 , N'PostSubmission' , N'GameRating' , N'Xap'  ), ( 3 , N'Presubmission' , N'GameRating' , NULL  ), 
                ( 4 , N'Presubmission' , N'TCRRule' , N'Xap'  ), ( 5 , N'PostSubmission' , NULL , N'Xap'  ), ( 6 , N'Submission' , NULL , N'Xap'  ) ;


SELECT * 
FROM #Final a

SELECT a.RwNum AS aId, b.RwNum AS bId
FROM #Final a
JOIN #Final b 
ON ( a.JobSource = b.JobSource AND a.RuleName = b.RuleName )
OR ( a.JobSource = b.JobSource AND a.PackageType = b.PackageType AND a.RuleName IS NULL )
WHERE a.RwNum <> b.RwNum



SELECT * 
FROM #Final AS f
WHERE NOT EXISTS 
        ( SELECT *
          FROM #Final AS a
          JOIN #Final AS b 
                  ON ( a.JobSource = b.JobSource AND a.RuleName = b.RuleName )
                  OR ( a.JobSource = b.JobSource AND a.PackageType = b.PackageType AND a.RuleName IS NULL )
          WHERE a.RwNum <> b.RwNum
                AND f.RwNum = IIF(a.RwNum > b.RwNum, a.RwNum , b.RwNum) )

---

Saeid Hasani [sqldevelop]