The integral does not admit a closed form, I am afraid. It is discussed in the vol. 2 of Bateman's "Higher Transcendental functions", section 7.7.3, formula 15, which gives
$$
2^{\mu + \nu} \alpha^{-\mu} \beta^{-\nu} \gamma^{\lambda + \mu+\nu} \Gamma\left(\nu+1\right) \int_0^\infty J_{\mu}(\alpha t) J_\nu(\beta t) \mathrm{e}^{-\gamma t} t^{\lambda -1} \mathrm{d} t = \sum_{m=0}^\infty \frac{\Gamma\left(2m+\lambda+\mu+\nu\right)}{m! \Gamma(m+\mu+1)} \cdot {}_2F_1\left(-m,-m-\mu; \nu+1; \frac{\beta^2}{\alpha^2}\right) \left( -\frac{\alpha^2}{4 \gamma^2} \right)^m
$$
In your case, $\lambda = 1$, $\mu=0$, $\nu=1$, $\gamma=1$:
$$
\frac{2}{\beta} \int_0^\infty J_0(\alpha t) J_1(\beta t) \mathrm{e}^{-t} \mathrm{d}t = \sum_{m=0}^\infty \frac{\Gamma\left(2m+2\right)}{m! \Gamma(m+1)} \cdot {}_2F_1\left(-m,-m; 2; \frac{\beta^2}{\alpha^2}\right) \left( -\frac{\alpha^2}{4} \right)^m
$$
By expanding the Bessel function $J_1(b t)$ in its defining series and integrating term-wise we can find other series representations:
$$
\int_0^\infty J_0(a t) J_1(b t) \mathrm{e}^{-t} \mathrm{d}t = \frac{b}{2} \sum_{m=0}^\infty \binom{2m+1}{m} \frac{\left(-\frac{b^2}{4}\right)^m}{(1+a^2)^{2m+3/2}} \cdot {}_2F_1\left(-m, -m-\frac{1}{2}; 1; -a^2\right)
$$
where, additionally, the Euler's transformation of the Gauss' hypergeometric function had been used.
EDIT:
I think the OP was referring to the recurrence relation $$\frac{d}{dx} \left(x^{-n}j_{n}(x) \right)=-x^{-n}j_{n+1}(x). \tag{1} $$
From $(1)$ it follows immediately that $$\begin{align}\int_{0}^{\infty}x^{-n} j_{n+1}(x) \, dx &= -x^{-n} j_{n}(x) \Bigg|^{\infty}_{0} \\ &=-x^{n} \sqrt{\frac{\pi}{2x}} \, J_{n+\frac{1}{2}}(x) \Bigg|^{\infty}_{0} \\ &= \lim_{x \downarrow 0} \, x^{-n} \sqrt{\frac{\pi}{2x}} \, J_{n+\frac{1}{2}}(x) \tag{2} \\ &=\lim_{x \downarrow 0} \, x^{-n} \sqrt{\frac{\pi}{2x}}\left(\frac{1}{\Gamma\left(n + \frac{3}{2}\right)} \left(\frac{x}{2}\right)^{n+ \frac{1}{2}} +\mathcal{O}\left(x^{n+ \frac{5}{2}} \right)\right) \tag{3} \\ &= \sqrt{\pi} \, 2^{-n-1} \, \frac{1}{\Gamma \left(n+ \frac{3}{2}\right)} \\ &= \sqrt{\pi} \, 2^{-n-1} \, \frac{2^{n+1}}{\sqrt{\pi} (2n+1)!!} \tag{4}\\ &= \frac{1}{(2n+1)!!}. \end{align}$$
$(1)$: http://dlmf.nist.gov/10.51#E3
$(2)$: https://en.wikipedia.org/wiki/Bessel_function#Asymptotic_forms
$(3)$: https://en.wikipedia.org/wiki/Bessel_function#Bessel_functions_of_the_first_kind:_J.CE.B1
$(4)$: http://mathworld.wolfram.com/DoubleFactorial.html (2)
This might not be the particular approach you were seeking, but it can be evaluated using a property of the Mellin transform.
Ramanujan's master theorem states that if $f(x)$ has an expansion of the form $$ f(x) = \sum_{k=0}^{\infty} \frac{\phi(k)}{k!} (-x)^{k} ,$$
then
$$ \int_{0}^{\infty} x^{s-1} f(x) \, dx = \Gamma(s) \phi(-s) $$
for the values of $s$ for which the integral converges.
The hypergeometric representation of the Bessel function of the first kind of order $\alpha$ is $$ J_{\alpha}(x) = \frac{(\frac{x}{2})^{\alpha}}{\Gamma(\alpha +1)} \ {}_0F_{1} \left(\alpha +1; - \frac{x^{2}}{4} \right) = \frac{(\frac{x}{2})^{\alpha}}{\Gamma(\alpha +1)} \sum_{k=0}^{\infty} \frac{\Gamma(\alpha + 1)}{\Gamma(\alpha +1+k)} \frac{(-\frac{x^{2}}{4})^{k}}{k!} .$$
So for $s+n+1 >0$ and $s <2$, we have
$$ \begin{align} \int_{0}^{\infty} x^{s-1} j_{n+1}(x) \, dx &= \int_{0}^{\infty} x^{s-1} \sqrt{\frac{\pi}{2x}} \, J_{n+\frac{3}{2}} (x) \, dx \\ &= \int_{0}^{\infty} x^{s-1} \sqrt{\frac{\pi}{2x}} \frac{(\frac{x}{2})^{n + \frac{3}{2}}}{\Gamma(n +\frac{5}{2})} \, {}_0F_{1} \left(n + \frac{5}{2}; - \frac{x^{2}}{4} \right) \, dx \\ &= \frac{\sqrt{\pi}}{2^{n+2}} \frac{1}{\Gamma(n+\frac{5}{2})} \int_{0}^{\infty} x^{s+n} \, {}_0F_{1} \left(n + \frac{5}{2}; - \frac{x^{2}}{4} \right) \, dx \\ &= \frac{\sqrt{\pi}}{2^{n+2}} \frac{1}{\Gamma(n+\frac{5}{2})} \int_{0}^{\infty} (2 \sqrt{u})^{s+n} \, {}_0F_{1} \left(n + \frac{5}{2}; - u \right) \, \frac{du}{\sqrt{u}} \\ &= \frac{ \sqrt{\pi} \ 2^{s-2}}{\Gamma(n+\frac{5}{2})} \int_{0}^{\infty} u^{\frac{s+n+1}{2}-1} \, {}_0F_{1} \left(n + \frac{5}{2}; - u \right) \, du \\ &= \frac{ \sqrt{\pi} \ 2^{s-2}}{\Gamma(n+\frac{5}{2})} \, \Gamma \left(\frac{s+n+1}{2} \right) \frac{\Gamma(n+ \frac{5}{2})}{\Gamma(n + \frac{5}{2} - \frac{s+n+1}{2})} \\ &= \sqrt{\pi} \ 2^{s-2} \, \Gamma \left(\frac{s+n+1}{2} \right) \frac{1}{\Gamma(\frac{4-s+n}{2})} . \end{align}$$
Now let $s= -n+1$.
Then
$$ \begin{align} \int_{0}^{\infty} x^{-n} j_{n+1}(x) \ dx &= \sqrt{\pi} \ 2^{-n-1} \Gamma (1) \, \frac{1}{\Gamma \left(n + \frac{3}{2} \right)} \\ &= \sqrt{\pi} \ 2^{-n-1} \frac{2^{n+1}}{\sqrt{\pi} (2n+1)!!} \tag{1} \\ &= \frac{1}{(2n+1)!!} \end{align}$$
$(1)$: http://mathworld.wolfram.com/DoubleFactorial.html (2)
Best Answer
Using the identity $$j_n(x)=\sqrt{\frac{\pi }{2x}} J_{n+\frac{1}{2}}(x)$$ $$\int x^2 \,j_n(x){}^2 \,dx=\frac{\pi}{2} \int x J_{n+\frac{1}{2}}(x){}^2 \,dx=\frac{\pi}{4} x^2 \left(J_{n+\frac{1}{2}}(x){}^2-J_{n-\frac{1}{2}}(x) J_{n+\frac{3}{2}}(x)\right)$$