Okay. Re-reading your code, I think that you only want to replace the paired bits on even bit boundaries?

Substitute this for the other regex.

$bits =~ s[(..)][     ## Look at every pair of bits
    $1 eq '00'        ## If they are 00 
        ? '11'        ## replace them 11
        : $1 eq '11'  ## If they are 11
            ? '00'    ## replace them with 00
            : $1      ## else leave them alone
]ge;
[download]

That will slow it down a bit, but it will still run quicker than splitting the string into and array etc.