I'd go for a KISS approach to apply multiple replacements of non nested pairs with placeholders.

0: The use of parentheses (indicates that the (writer [considered] the {information}) less <important—almost> an afterthought).

1: The use of parentheses (indicates that the (writer  %0% the %1%) less %2% an afterthought).

2: The use of parentheses (indicates that the %3% less %2% an afterthought).

3: The use of parentheses %4%.

This can be done by repeating one simple regex over and over and storing the matches in an array. Afterwards you just need to reconstruct the tree again.

NB: I just used %n% for visualization. Using something like \0 is far better here.

HTH :)