Alright, so, using Corollary 9 in the chapter on Nielsen's method in D.L Johnson's book, as Derek Holt suggested, I got a pretty clear idea on how to solve that problem. My only issue is that I am not supposed to know about the concepts such as the Nielsen transformation and being N-reduced. However, I believe I can form a pretty concrete proof, please let me know if there are any mistakes.
Take $B_i$, a free basis of $C_i$.
Suppose that we have $w \in X_i$ such that $w \in C_{i+1}$, as the homomorphisms switching the elements of $X_i$ with eachother are automorphisms, $X_i \subset C_{i+1}$, since $C_{i+1}$ is characteristic. However, then $C_i \leq C_{i+1} $, which is impossible as they are proper subgroups.
Now take $w_0 \in X_i$ such that $l(w_0)\leq l(w), w\in X_i$, with $l$ the length using the basis of F.
We can assume $l(w_0) \leq l(w), w\in C_i$. Or we transform the basis to have $w_0$ in it which gives an automorphism.
Now, we have that $l_i :=l(w_0)=min\{l(w), w \in C_i\}$ and for all $w \in C_i$ such that $l(w)=l_i$, we can once again create a new basis in which $w$ belong, and we can create an automorphism between the basis so $w \notin C_{i+1}$.
Now, we have proven that the shortest $w \in C_{i+1}$ has length $l(w)>l_i$.
Using this, we have $1 = l_1 < l_2 < l_3 < ...$. So if we take $v \in F, l(v)=k$, then $v \notin C_{k+1}$.
So $\cap C_i = 1$