At first, according your assumption, $\{X(t),t\in [0,1]\}$ is a Gaussian process and continuous in probability
on $[0,1]$, then $\{X(t),t\in [0,1]\}$ is continuous in mean square on $[0,1]$
and $\sigma^2(t)=\mathsf{E}[X^2(t)]$ is also continuous on $[0,1]$.
In the following we consider a separable real Gaussian process $Y=\{Y(t),t\in[0,1]\}$ with $\mathsf{E}[Y(t)]=0$ and covariance function
\begin{align*}
B(s,t)&=\mathsf{E}[Y(s)Y(t)]\\
&=\begin{cases}
\displaystyle{\int_{0}^{\infty}\frac{\cos (\lambda(t-s))}{2(e+\lambda) [\log(e+\lambda)]^{3/2}}}\mathrm{d}\lambda & 0\le s,t< \tfrac12,\\
0, & 0\le s< \tfrac12, \tfrac12\le t\le 1, \\
0, & 0\le t< \tfrac12, \tfrac12\le s\le 1, \\
\displaystyle{\int_{0}^{\infty}\frac{3\cos (\lambda(t-s))}{2(e+\lambda) [\log(e+\lambda)]^{5/2}}}\mathrm{d}\lambda & \tfrac12\le s,t\le 1
\end{cases}
\end{align*}
Then
\begin{equation*}
B(t,t)=1,\quad t\in [0,1].
\end{equation*}
Using Belyaev's result in paper "Local properties of the sample functions of stationary Gaussian processes, Theor. Prob. Appl., 5, 117-120.(1960) ", almost all sample fonctions of $Y$ are continuous in $[\frac12,1]$ and unbounbed on any interval $I\subset [0,\frac12)$.
Now let
\begin{gather*}
X(t)=\sigma(t)Y(t),\qquad 0\le t\le 1, \tag{1}\\
\mathsf{E}[X(s)X(t)]=\sigma(s)\sigma(t)B(s,t),\qquad 0\le s,t \le 1.
\end{gather*}
It is easy to verify that $\mathsf{E}[X(s)X(t)]$ is continuous on $[0,1]\times[0,1]$ and
$\{X(t),t\in [0,1]\}$ is continuous in mean. Furthermore, $\{X(t),t\in [0,1]\}$ satisfy all conditions required above
but the No.1: $\{X(t),t\in [0,\tfrac12)\}$ is not right-continuous a.s. and
$\{X(t),t\in [\tfrac12,1]\}$ is right-continuous a.s.. Meanwhile,
almost all sample functions of $X$ are unbounded on any interval $I\subset [0,\frac12)$, hence there is a discontinuous of second kind at $t=1/2$.
Sorry, I couldn't provide an example satisfying all conditions required above.
Remark: Regarding the discontinuity of stationary Gaussian process, please refer
the paper: R. L. Dobrushin, Properties of sample functions of a stationary Gaussian process, Theory Prob. Applications, 5 1960, pp. 120-122.