You probably want sprintf, sprintf("%04d",$number) will return it in a 4 digit number padded by zeros, then you can do a test to see if the number is greater than 9999 and handle it according. also, ++ will maintain the zeros if they are in the variable... i.e.

$a = '0001';
$a++;
print $a;
0002
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then you can just use a regexp or substring to put chop and edit the version number.