I suppose that asking publicly somehow gave me the inspiration to figure it out after I had been stuck with it for a while. The answer is actually fairly straightforward. We can construct the Gram matrix for the sets of vectors
$$\{[e_{\alpha_{i_1}} [e_{\alpha_{i_2}} [\cdots e_{\alpha_{i_N}}]]]\}$$
and
$$\{[f_{\beta_{i_1}} [f_{\beta_{i_2}} [\cdots f_{\beta_{i_N}}]]]\}$$
using simple properties of the invariant form and the Jacobi identity, by induction on the height of $\alpha = \sum k_i \alpha_i$ where $\operatorname{ht}(\alpha) = \sum k_i$. Suppose it has been calculated for height $N-1$. Then let
$$f_i := f_{\beta_i}\\
f_{>i} := [f_{i+1} [\cdots f_{N}]]$$
and analogous definitions for $e_j, e_{> i}, e_{< N}$ etc. We can then calculate
$$(f_{\ge 1}| e_{\ge 1}) = ([f_1, f_{> 1}]|[e_1 , e_{> 1}])\\
= (f_1 | [f_{> 1}, [e_1 , e_{> 1}]])\\
= (f_1 | [[f_{>1}, e_1],e_{>1} ]) + ([f_1, e_1] | [f_{>1},e_{> 1}])\\
= (f_1 | [[f_{>1}, e_1],e_{>1} ]) + \delta_{\alpha_1, \beta_1}([h_{\alpha_1} f_{> 1}] | e_{> 1})\\
= (f_1 | [[f_{>1}, e_1],e_{>1} ]) + \tilde{c} (f_{> 1} | e_{> 1})$$
Then we just use repeated applications of Jacobi and $[e_i, f_j] = \delta_{\alpha_i, \beta_j} h_{\alpha_i}$ to show that
$$[f_{>1}, e_1] = \sum_{i=2}^N c_i f_{> i} + d [f_2 [ \cdots f_{N-1}]]$$
for easily computable constants $c_i$ and $d$. Thus our sum becomes
$$\sum_{i = 2}^N c_i ([f_1, f_{> i}] | e_{>1}) + d (f_{<N}| e_{>1}) + \tilde{c} (f_{>1} | e_{> 1})$$
for constants $c_i, d, \tilde{c}$ straightforwardly computable. Thus we have written the pairing in terms of pairings of lower height. From here we can just use linear algebra to pick a basis so the Gram matrix has full rank on this subspace.