Is this all you're trying to do?
$ awk '{split($2,d,"/"); $2="20"d[3]"-"d[1]"-"d[2]}1' file
1 2013-01-04 02:20:07 PM 21.843 24.360 981.5
2 2013-01-04 02:25:07 PM 21.509 27.048 335.1
3 2013-01-04 02:30:07 PM 19.555 31.441 335.1
4 2013-01-04 02:35:07 PM 18.628 32.154 335.1
5 2013-01-04 02:40:07 PM 18.152 31.782 327.2
6 2013-01-04 02:45:07 PM 17.962 34.723 327.2
7 2013-01-04 02:50:07 PM 17.867 33.008 335.1
8 2013-01-04 02:55:07 PM 17.819 35.722 327.2
9 2013-01-04 03:00:07 PM 17.819 33.989 327.2
10 2013-01-04 03:05:07 PM 17.796 36.143 327.2
or do you need to change the time format too?
awk '{split($2,d,"/"); $2="20"d[3]"-"d[1]"-"d[2];
split($3,t,":"); if(sub(/PM /,"")) t[1]+=12; $3=t[1]":"t[2]":"t[3]
}1' file
1 2013-01-04 14:20:07 21.843 24.360 981.5
2 2013-01-04 14:25:07 21.509 27.048 335.1
3 2013-01-04 14:30:07 19.555 31.441 335.1
4 2013-01-04 14:35:07 18.628 32.154 335.1
5 2013-01-04 14:40:07 18.152 31.782 327.2
6 2013-01-04 14:45:07 17.962 34.723 327.2
7 2013-01-04 14:50:07 17.867 33.008 335.1
8 2013-01-04 14:55:07 17.819 35.722 327.2
9 2013-01-04 15:00:07 17.819 33.989 327.2
10 2013-01-04 15:05:07 17.796 36.143 327.2