The Lagrangian for your 1D pitch system is $\mathcal{L} := T - U$, which is
$$
\mathcal{L} = \frac{1}{2}(mb^2 + Ma^2)\dot{\phi}^2 + \frac{1}{2}J\dot{\theta}^2 + (Ma - mb)g\sin\phi
$$
The Euler-Lagrange Equations are
$$
\frac{d}{dt}\bigg(\frac{\partial\mathcal{L}}{\partial \dot{q}_k}\bigg) + \frac{\partial\mathcal{L}}{\partial q_k} = Q_k
$$
This gives the EOM
$$
(mb^2 + Ma^2)\ddot{\phi} + (Ma - mb)g\cos\phi = -Tb = -k_1\dot{\theta}^2b
$$
Under a small angle approximation, $\cos\phi \approx 1$, so this leaves
$$
(mb^2 + Ma^2)\ddot{\phi} + (Ma - mb)g = -k_1b\dot{\theta}^2,
$$
or in another form,
$$
\ddot{\phi} = \frac{mb-Ma}{mb^2 + Ma^2}g - \frac{k_1b}{mb^2 + Ma^2}\dot{\theta}^2 = \beta_1 - \beta_2\dot{\theta}^2.
$$
Now, I don't know if these are the correct equations for your system, but based on what you outlined in your question, this is what the EOM are for $\phi(t)$.
You also have a coupled system of ODE's for $I(t)$ and $\theta(t)$ since from $\dot{\theta} = \omega_2$ it follows that
$$
\begin{align}
\ddot{\theta} &= \frac{K}{J}I - \frac{k_2}{J}\dot{\theta}^2\\
\dot{I} &= \frac{E}{L} - \frac{R}{L}I - \frac{k_1}{L}\dot{\theta}
\end{align}
$$
Again, this is all based off your model that you wrote in the problem statement. So, in total, you have three ODE's for the three variables $\theta,\phi,I$. Given that this system of 3 ODE's is nonlinear, there is no analytical solution. What you can do to simulate this is solve the system in MATLAB for example using ODE45 or just any differential equaton solver.
If you want to linearize this system, you can do the following. First, put the system in state space form, i.e. let $x = [\phi,\dot{\phi},\theta,\dot{\theta},I]^\intercal$ so that the full dynamics are
$$
\begin{align}
\dot{x}_1 &= x_2\\
\dot{x}_2 &= \beta_1\cos x_1 - \beta_2 x_4^2\\
\dot{x}_3 &= x_4\\
\dot{x}_4 &= \frac{K}{J}x_5 - \frac{k_2}{J}x_4^2\\
\dot{x}_6 &= \frac{E}{L} - \frac{R}{L}x_5 - \frac{k_1}{L}x_4.
\end{align}
$$
Notice that the nonlinear equations are the second one and the fourth one. So right now you system like $\dot{x} = f(x)$, where $f(x)$ is a nonlinear function (5 by 1 vector). To linearize this sytem into the form $\dot{x} = Ax$, you can set
$$
A = \bigg[\frac{\partial f}{\partial x}\bigg]_0,
$$
evaluated at some nominal conditions, which will give a 5 by 5 matrix. In your case this gives
$$
A =
\begin{bmatrix}
0 & 1 & 0 & 0 & 0\\
-\beta_1\sin x_1 & 0 & 0 & -2\beta_2 x_4 & 0\\
0 & 0 & 0 & 1 & 0\\
0 & 0 & 0 & -2\frac{k_2}{J}x_4 & \frac{K}{J}\\
0 & 0 & 0 & -\frac{k_1}{L} & -\frac{R}{L}
\end{bmatrix}_0
$$
So you need to come up with some reference point for linearization for $\phi$ and $\dot{\theta}$, and then you can simulate the linearized system.