It would have helped if you are clear with your requirements. Here is an updated DFSORT/ICETOOL JCL which will give you the desired results . I eliminated the duplicate records from file1 just based on the Dataset name.
//STEP0100 EXEC PGM=ICETOOL
//TOOLMSG DD SYSOUT=*
//DFSMSG DD SYSOUT=*
//FB50 DD DSN=Your input1 FB 50 byte file,DISP=SHR
//TM96 DD DSN=&&TM96,DISP=(,PASS),SPACE=(CYL,(1,1),RLSE)
//FB96 DD DSN=Your input2 FB 96 byte file,DISP=SHR
// DD DSN=&&TM96,DISP=SHR,VOL=REF=*.TM96
//OUT DD SYSOUT=*
//TOOLIN DD *
SORT FROM(FB50) USING(CTL1)
SPLICE FROM(FB96) TO(OUT) ON(13,44,CH) WITH(1,3) USING(CTL2)
//CTL1CNTL DD *
SORT FIELDS=(6,44,CH,A),EQUALS
SUM FIELDS=NONE
OUTFIL FNAMES=TM96,BUILD=(1,3,13:6,44,96:X)
//CTL2CNTL DD *
OUTFIL FNAMES=OUT,
BUILD=(01,03, $ FILE-1 FIELD-1
3X, $ 3 BLANKS
13,44, $ DATASET NAME
3X, $ 3 BLANKS
04,06, $ FILE-2 FIELD-1
3X, $ 3 BLANKS
60,10, $ FILE-2 FIELD-3
3X, $ 3 BLANKS
73,10, $ FILE-2 FIELD-4
3X, $ 3 BLANKS
86,05, $ FILE-2 FIELD-5
4X, $ 3 BLANKS
95,02) $ FILE-2 FIELD-6
//*
//TOOLMSG DD SYSOUT=*
//DFSMSG DD SYSOUT=*
//FB50 DD DSN=Your input1 FB 50 byte file,DISP=SHR
//TM96 DD DSN=&&TM96,DISP=(,PASS),SPACE=(CYL,(1,1),RLSE)
//FB96 DD DSN=Your input2 FB 96 byte file,DISP=SHR
// DD DSN=&&TM96,DISP=SHR,VOL=REF=*.TM96
//OUT DD SYSOUT=*
//TOOLIN DD *
SORT FROM(FB50) USING(CTL1)
SPLICE FROM(FB96) TO(OUT) ON(13,44,CH) WITH(1,3) USING(CTL2)
//CTL1CNTL DD *
SORT FIELDS=(6,44,CH,A),EQUALS
SUM FIELDS=NONE
OUTFIL FNAMES=TM96,BUILD=(1,3,13:6,44,96:X)
//CTL2CNTL DD *
OUTFIL FNAMES=OUT,
BUILD=(01,03, $ FILE-1 FIELD-1
3X, $ 3 BLANKS
13,44, $ DATASET NAME
3X, $ 3 BLANKS
04,06, $ FILE-2 FIELD-1
3X, $ 3 BLANKS
60,10, $ FILE-2 FIELD-3
3X, $ 3 BLANKS
73,10, $ FILE-2 FIELD-4
3X, $ 3 BLANKS
86,05, $ FILE-2 FIELD-5
4X, $ 3 BLANKS
95,02) $ FILE-2 FIELD-6
//*