I derived these formulas with the Laurent series and Euler-Maclaurin summation formula. I can demonstrate this later if anyone's curious. I'm wondering if there is another way. I'm also interested in finding generalized formulas.
$$\lim\limits_{\alpha\to 0}\left[\frac{\ln\left(\alpha\right)}{2}+\int_{\alpha}^{\infty}\frac{1}{t\left(e^{t}+1\right)}dt\right]=\frac{1}{2}\left(\ln\left(\pi\right)-\ln\left(2\right)-\gamma\right)$$
$$\lim\limits_{\alpha\to 0}\left[\frac1\alpha+\frac{\ln\left(\alpha\right)}{2}-\int_{\alpha}^{\infty}\frac{1}{t\left(e^{t}-1\right)}dt\right]=\frac{1}{2}\left(\ln\left(\pi\right)+\ln\left(2\right)-\gamma\right)$$
A manipulation of these equations yields
$$\lim\limits_{s\to -1}\left[\frac{1}{\ln|s|}+\left(-\frac{1}{s+1}+\frac{1}{2}\right)\ln|\ln|s||+\int_{s}^{\infty}\frac{\ln\left(\ln\left(u\right)\right)}{\left(u+1\right)^{2}}du\right]=\frac{1}{2}\left(\ln\left(\pi\right)-3\ln\left(2\right)-\gamma\right)$$
$$\lim\limits_{s\to 1}\left[\frac{1}{\ln\left(s\right)}+\left(\frac{1}{s-1}+\frac{1}{2}\right)\ln\left(\ln\left(s\right)\right)-\int_{s}^{\infty}\frac{\ln\left(\ln\left(u\right)\right)}{\left(u-1\right)^{2}}du\right]=\frac{1}{2}\left(\ln\left(\pi\right)+\ln\left(2\right)-\gamma\right)$$
Here is my elementary method of deriving these:
Begin with the Euler-Maclaurin summation formula:
$$ \begin{align} \frac{1}{h}\int_a^b f(t)dt &=\sum_{k=0}^n f(kh+a)-\left(\frac{f(a)+f(b)}{2}\right) \\&-\sum_{k=1}^n \frac{h^{2k-1}B_{2k}}{(2k)!} \left(f^{(2k-1)}(b)-f^{(2k-1)}(a)\right) \\&-R \end{align} $$
where $h=\frac{b-a}{n}$ and $R$ is the remainder term. Letting $n=\frac{b-a}{x}$ and rearranging we get
$$ \begin{align} \sum_{k=1}^{(b-a)/x} \frac{x^{2k-1}B_{2k}}{(2k)!} \left(f^{(2k-1)}(b)-f^{(2k-1)}(a)\right) &=\sum_{k=0}^{(b-a)/x} f(kx+a)-\left(\frac{f(a)+f(b)}{2}\right) \\&-\frac{1}{x}\int_a^b f(t)dt \\&-R \end{align} $$
Limiting $b\to 0$ and $a\to -\infty$, we have
$$ \begin{align} \lim\limits_{\substack{% a \to -\infty\\ b \to 0}} \sum_{k=1}^{-a/x} \frac{x^{2k-1}B_{2k}}{(2k)!} \left(f^{(2k-1)}(b)-f^{(2k-1)}(a)\right) &=\lim\limits_{\substack{% a \to -\infty\\ b \to 0}}\left(\sum_{k=0}^{-a/x} f(kx+a)-\left(\frac{f(a)+f(b)}{2}\right)-\frac{1}{x}\int_a^b f(t)dt\right) \end{align} $$
The remainder disappears as $n\to\infty$. Now make a variable substitution in the limit $a\to -ax$.
$$ \begin{align} \lim\limits_{\substack{% a \to \infty\\ b \to 0}}\sum_{k=1}^{a} \frac{x^{2k-1}B_{2k}}{(2k)!} \left(f^{(2k-1)}(b)-f^{(2k-1)}(-ax)\right) &=\lim\limits_{\substack{% a \to \infty\\ b \to 0}}\left(\sum_{k=0}^{a} f((k-a)x)-\left(\frac{f(-ax)+f(b)}{2}\right)-\frac{1}{x}\int_{-ax}^b f(t)dt\right) \\&=\lim\limits_{\substack{% a \to \infty\\ b \to 0}}\left(\sum_{k=0}^{a} f(-kx)-\left(\frac{f(-ax)+f(b)}{2}\right)-\frac{1}{x}\int_{-ax}^b f(t)dt\right) \end{align} $$
Now use the following hint.
$$\frac{1}{z(e^z-1)}=\frac{1}{z^2}-\frac{1}{2z}+\sum_{k=1}^\infty\frac{B_{2k}}{(2k)!}z^{2k-2}$$
which when we integrate we get
$$\begin{align} \int_x^\infty\frac{1}{z(e^z-1)}dz &=K-\left(-\frac{1}{x}-\frac{\ln{|x|}}{2}+\sum_{k=1}^\infty\frac{B_{2k}}{(2k)!(2k-1)}x^{2k-1}\right) \end{align}$$
Where $K$ stands for the integral evaluated at $\infty$.
Let $f(x)=\text{Ei}\left(x\right)-\ln\left|x\right|-\gamma$. Note that $\lim\limits_{t\to 0}f^{(m)}(t)=\frac1m$ and $\lim\limits_{t\to -\infty}f^{(m)}(t)=0$ for $m\ge1$. Further note that $\lim\limits_{t\to 0} f(t) = 0$ so we may substitute the sum: $\sum_{k=0}^{a} f(-kx)=\sum_{k=1}^{a} f(-kx)$. Now we have
$$ \begin{align} \sum_{k=1}^\infty\frac{B_{2k}}{(2k)!(2k-1)}x^{2k-1} &=\lim\limits_{\substack{% a \to \infty\\ b \to 0}}\left(\sum_{k=1}^{a} f(-kx)-\left(\frac{f(-ax)+f(b)}{2}\right)-\frac{1}{x}\int_{-ax}^b f(t)dt\right) \\&=\lim\limits_{\substack{% a \to \infty\\ b \to 0}}\left(\sum_{k=1}^{a}\text{Ei}(-kx)-\sum_{k=1}^{a}\ln\left|-kx\right|-\sum_{k=1}^{a}\gamma-\left(\frac{f(-ax)+f(b)}{2}\right)-\frac{1}{x}\int_{-ax}^b f(t)dt\right) \\&=-\int_x^\infty\frac{1}{z(e^z-1)}dz+\lim\limits_{\substack{% a \to \infty\\ b \to 0}}\left(-a\ln|x|-\ln|a!|-a\gamma-\left(\frac{f(-ax)+f(b)}{2}\right)-\frac{1}{x}\int_{-ax}^b f(t)dt\right) \\&=-\int_x^\infty\frac{1}{z(e^z-1)}dz+\frac{1}{x}+\frac{\ln\left|x\right|}{2}+\frac{1}{2}\left(\gamma-\ln\left(2\pi\right)\right) \end{align} $$
(The limit is tricky which is why I left out some steps). Therefore
$$\begin{align} \int_x^\infty\frac{1}{z(e^z-1)}dz=\frac12 (\gamma-\ln(2\pi))+\frac{1}{x}+\frac{\ln{|x|}}{2}-\sum_{k=1}^\infty\frac{B_{2k}}{(2k)!(2k-1)}x^{2k-1} \end{align}$$
We can derive the other equation with $f(x)=-\text{Ei}(x)+2\text{Ei}(2x)-\ln|4x|-\gamma$.
For the first Limit, write ($s\rightarrow 1_-$, $a\rightarrow 0_+$ in this order)
$$ I(s,a)=J_1(s)-J_2(s,a)=\int_0^{\infty}dx\frac{x^{-s}}{(e^x+1)}-\frac12\int_0^{\alpha}x^{-s}(1+O(x))dx $$
the first integral is a integral repesentation of the Dirichlet eta function (Proof: Taylor Expansion of the denonominator), which is related to the Riemann Zeta function as follows $\eta(s)=(2^s-1)\zeta(s)$, which is easily seen from the respective series representation. We therefore have
$$ I(s,a)=\Gamma(1-s)\eta(s)+\frac{a^{-s+1}}{2(s-1)}+O(a^{2-s}(s-2)^{-1})=\\ \color{red}{\Gamma(1-s)(2^s-1)\zeta(s)}+\color{blue}{\frac{a^{-s+1}}{2(s-1) }}+\color{green}{O(a^{2-s}(s-2)^{-1})}\quad (\star) $$
Taking the limit in $s$ we get (Proof: expand both sides of the functional equation of the Zetafunction around $s=1$ and use $\Gamma(s)=1-\gamma(s-1)+O((s-1)^2)$ ),
$$ \color{red}{\Gamma(1-s)(2^s-1)\zeta(s)}=\color{red}{-\frac 1{2 (s-1)}+\frac{1}2 \left(-\gamma+\log(\pi/2)\right)+O(s-1)} $$
and furthermore $$ \color{blue}{\frac{a^{-s+1}}{2(s-1)}}=\color{blue}{\frac 1{2 (s-1)}-\frac{1}2\log(a)+O(s-1)} $$
as well as
$$ \color{green}{O(a^{2-s}(s-2)^{-1})}=\color{green}{a+O(s-1)} $$
the green part is clearly negligible as $a\rightarrow 0+$
so, as we subsitute back into $(\star)$ we get in total
$$ \lim_{a\rightarrow 0+} (I(1,a)+\color{blue}{\frac{1}2\log(a)})=\color{red}{\frac{1}2 \left(-\gamma+\log(\pi/2)\right)} $$
as expected (note how the singular term exactly cancels, this was the motivation for the inital split of the integral).
The second Limit should be computable by the same method, taking one more term in the expansions of the different terms.
Edit: the singular part of the (exponentials) in the second Limit is $1/t+1/2$ which has to be substituted into $J_2(s,a)$