while ( <IN_FILE> ) {
   s{
     (?:^\ +|\ +$)
    |(?:\:000[A,P]M)
    |(?:99991231)
    |(?:Jan\ 1\ 1900\ 12:00:00)
   }{}gx;
   s/[ ]*\~\t\~[ ]*/~/g;
   print OUT_FILE $_;
}
close IN_FILE;
## and unlink() the filename for IN_FILE
## then rename() outfile to infile.