I agree with Tilly, that you should be assigning to a hash, rather than using symbolic references.
That said, the reason your code doesn't work is twofold. First, in "\$$stuff{$1} = $2", $stuff{$1} is interpolated as a value from %stuff, whereas you're trying to use $stuff as a symbolic reference. Second, the values of $1 and $2 are interpolated and then evalled, when the values may not be valid Perl code. (If $2 holds the string '+++++', for example, your eval won't compile.)
On the one hand, a correct line would be:
eval "\$$stuff\{\$1} = \$2";
On the other hand, the eval is unnecessary:
${$stuff}{$1} = $2;
On the gripping hand, the symbolic ref is also unnecessary, as previously stated:
$values{$stuff}{$1} = $2;
I hope that's helpful!
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