My tutorial on look-ahead and look-behind covers this. You're specifying that the open tag is not followed immediately by another open tag; you want to specify that it's followed by any arbitrary text that isn't an open tag. This s/// expression should do what you want:

$x =~ s{(?<=<td>)((?:(?!<td>).)*)3((?:(?!</td>).)*)(?=</td>)}{$1a$2};
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Update: I should have broken this down in commented style (I also note that I could have done lookahead for everything after the 3):

$x =~ s{(?<=<td>)         # Start match with open-tag
        (                 # Capture
          (?:(?!<td>).)*  #  Any number of characters that do not star
+t an open-tag
        )3                # Close capture; match literal 3
        (?=               # Look ahead to match
          (?:(?!</td>).)* #  Any number of characters that do not star
+t a close-tag
         </td>            #  then a close-tag
        )}                # End lookahead and pattern
       {$1a}x;
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