Following the suggestion of Kaveh, I am putting my comment as an (expanded) answer.
Concerning $Q1$, a word of caution is in order: even logarithmic depth if far from being understood, not speaking about poly-logarithmic. So, in the non-monotone world, the real problem is much less ambitious:
Beating Log-depth Problem: Prove a super-linear(!) lower bound for $NC^1$-circuits.
The problem remains open (for now more than 30 years) even for
linear $NC^1$-circuits. These are fanin-
$2$ circuits over the basis
$\{\oplus,1\}$, and they compute linear transformations
$f(x)=Ax$ over
$GF(2)$. Easy counting show that almost all matrices
$A$ require
$\Omega(n^2/\log n)$ gates, in any depth.
Concerning $Q2$: Yes, we have
some algebraic/combinatoric measures, lower bounds on which
would beat log-depth circuits. Unfortunately, so far,
we cannot prove large enough bounds on these measures. Say,
for linear $NC^1$-circuits, such a measure is the rigidity $R_A(r)$ of the matrix $A$. This is the smallest number of entries of $A$ that one needs to change in order to reduce the rank to $r$.
It is easy to show that $R_A(r)\leq (n-r)^2$ holds for every boolean $n\times n$ matrix $A$, and Valiant (1977) has shown that this bound is tight for almost all matrices.
To beat log-depth circuits, it is enough to exhibit a sequence of boolean $n\times n$ matrices $A$ such that
$R_A(\epsilon n)\geq n^{1+\delta}$ for constants $\epsilon,\delta>0$.
The best we know so far are matrices
$A$ with
$R_A(r)\geq (n^2/r)\log(n/r)$. For Sylvester matrices (i.e. inner product matrices), the lower bound of
$\Omega(n^2/r)$ is
easy to show.
We have combinatorial measures for general (non-linear) $NC^1$-circuits, as well For a bipartite $n\times n$
graph $G$, let $t(G)$ be the smallest number $t$ such that $G$ can be written as an intersection
of $t$ bipartite graphs, each being a union of at most $t$ complete bipartite graphs. To beat
the general log-depth circuits, it would be enough to find a sequence of graphs with
$t(G_n)\geq n^{\epsilon}$ for a constant $\epsilon >0$
(see, e.g.
here on how this happens). Again, almost all graphs have
$t(G)\geq n^{1/2}$. However, the best remains a lower bound
$t(G)\geq \log^3 n$ for Sylvester matrices, due to
Lokam.
Finally, let me mention that we even have a "simple" combinatorial measure (quantity) a weak (linear) lower bound on which would yield even exponential(!) lower bounds for non-monotone circuits. For a bipartite $n\times n$ graph $G$, let $c(G)$ be the smallest number of
fanin-$2$ union ($\cup$) and intersection ($\cap$) operations required to produce $G$ when starting from stars; a star is a set of edges joining one vertex with all vertices on the other side. Almost all graphs have $c(G)=\Omega(n^2/\log n)$. On the other hand, a lower bound of
$c(G_n)\geq (4+\epsilon)n$ for a constant $\epsilon>0$
would imply a lower bound
$\Omega(2^{N/2})$ on the non-monotone circuit complexity of an explicit boolean function
$f_G$ of
$N$ variables. If
$G$ is
$n\times m$ graph with
$m=o(n)$, then even a lower bound
$c(G_n)\geq (2+\epsilon)n$ is enough (again, see, e.g. hereon how this happens). Lower bounds
$c(G)\geq (2-\epsilon)n$ can be shown for relatively simple graphs. The problem, however, is to do this with "
$-\epsilon$" replaced by "
$+\epsilon$". More combinatorial measures lower-bounding circuit complexity (including the
$ACC$-circuits)
can be found in the
[book](https://web.vu.lt/mif/s.jukna/boolean/index.html).
P.S. So,
are we by a constant factor of $2+\epsilon$ from showing $P\neq NP$?
Of course - not.
I mentioned this latter measure $c(G)$ only to show that one should treat "amplification" (or "magnification") of lower bounds with a healthy portion of skepticism: even though the bounds we need look "innocently", are much smaller (linear) than almost all graphs require (quadratic), the inherent difficulty of proving a (weak) lower bound may be even bigger. Of course, having found a combinatorial measure, we can say something about what properties of functions make them computationally hard. This may be useful for proving an indirect lower bound: some complexity class contains a function requiring large circuits or formulas. But the ultimate goal is to come up with an explicit hard function, whose definition does not have an "algorithmic smell", does not have any hidden complexity aspects.