You gave a perfectly valid and easy solution in your question: split and join. Possibly something like this, illustrated under the Perl debugger:

  DB<1> $line = "T1 CONT 11 100.00 0 0.00 | T2 IEB 11 100.00 0 0.00 | 
+T3 IEB 11 100.00 0 0.00 | T4 ICBO 11 100.00 0 0.00 | T5 ICBO 11 100.0
+0 0 0.00 | T6 BVEB 11 100.00 0 0.00 | T7 VFBE 11 100.00 0 0.00 | T8 V
+FBE 11 100.00 0 0.00 |";

  DB<2> @fields = split /\|/, $line;

  DB<3> x @fields
0  'T1 CONT 11 100.00 0 0.00 '
1  ' T2 IEB 11 100.00 0 0.00 '
2  ' T3 IEB 11 100.00 0 0.00 '
3  ' T4 ICBO 11 100.00 0 0.00 '
4  ' T5 ICBO 11 100.00 0 0.00 '
5  ' T6 BVEB 11 100.00 0 0.00 '
6  ' T7 VFBE 11 100.00 0 0.00 '
7  ' T8 VFBE 11 100.00 0 0.00 '
  DB<4> $new_string = join " ", @fields[0,2,4,6,1,3,5,7];

  DB<5> print $new_string;
T1 CONT 11 100.00 0 0.00   T3 IEB 11 100.00 0 0.00   T5 ICBO 11 100.00
+ 0 0.00   T7 VFBE 11 100.00 0 0.00   T2 IEB 11 100.00 0 0.00   T4 ICB
+O 11 100.00 0 0.00   T6 BVEB 11 100.00 0 0.00   T8 VFBE 11 100.00 0 0
+.00
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If you don't want the extra-spaces added between the temporary array elements, you can change it to something like this:

  DB<8> @fields = split /\| ?/, $line;

  DB<9> $new_string = join "", @fields[0,2,4,6,1,3,5,7];

  DB<10> print $new_string;
T1 CONT 11 100.00 0 0.00 T3 IEB 11 100.00 0 0.00 T5 ICBO 11 100.00 0 0
+.00 T7 VFBE 11 100.00 0 0.00 T2 IEB 11 100.00 0 0.00 T4 ICBO 11 100.0
+0 0 0.00 T6 BVEB 11 100.00 0 0.00 T8 VFBE 11 100.00 0 0.00
[download]