How about using a flip-flop operator?

while (<DATA>) {
  /# input for/ .. s/1\.00/5/g;
  print;
}
__DATA__
# input for Data

1.00  0.99  0.92
1.00 -0.22  0.61
[download]

or, to avoid warnings about "useless" use of flop,

use strict;
use warnings;
while (<DATA>) {
  if (/# input for/ .. /\d/) { s/1\.00/5/g }
  print;
}
__DATA__
# input for Data

1.00  0.99  0.92
1.00 -0.22  0.61
[download]