Currently we require the Fourier transform $g(p)$ of $f(x)=J_a(be^{-x}), a,b>0$ $$g(p)=\frac{1}{\sqrt{2\pi}} \int_{-\infty}^{\infty}e^{ipx} f(x) dx$$ We could not find it in Tables and Handbooks. Mathematica gives it in terms of Gamma functions and Gauss Hyper geometric function. A closer look suggested that Hypergeometric function was actually a hoax. As we were finally interested in $|g(p)|^2$, it was a pleasant surprise to get $$|g(p)|^2=\frac{1}{2\pi(p^2+a^2)},~~~~~(1)$$ which is independent of $b$ !, even the verification of (1) by
Mathematica in analytic mode for various sets of $a,b,p$ has been time consuming.
The question is how to prove (1) and get $g(p)$ by hand?
EDIT: By Integrate of Mathematica, I finally get $$g(p)=\frac{1}{2\sqrt{2\pi}} \left(\frac{2}{b}\right)^{ip} \frac{\Gamma[(a+ip)/2]}{\Gamma[1+(a-ip)/2]}$$ EDIT: Here is the Mathematica out put, see the pre=factor of hypergeometric function is 0.
g(p)=1/2 Gamma[ 1/2 (a + I p)] ((2^(I p) (1/b^2)^((I p)/2))/ Gamma[1/2 (2 + a - I p)] + 2^-a (-(1/b^2)^(-a/2) + b^ a) HypergeometricPFQRegularized[{1/2 (a + I p)}, {1 + a, 1/2 (2 + a + I p)}, -(b^2/4)])
A Bessel function (of any kind) $f(z)$ satisfies the ODE $$ w^2 f''(w) + w f'(w) + (w^2 - a^2) f(z) = 0. $$ Making the variable transformation $w = be^{-x}$ leads to the following ODE satisfied by $f(x) = J_a \left(be^{-x}\right)$: $$ f''(x) + \left(b^2 e^{-2x} - a^2 \right) f(x) = 0 $$ Now we can take the Fourier transform of this ODE. Assuming that the Fourier transform $g(p) = \mathcal{F}\left[ f(x) \right]$ can be analytically continued into the complex plane as $$ g(z) = \int_{-\infty}^{\infty} e^{izx} f(x) \, dx, $$ the Fourier transform of $e^{-2x} f(x)$ is $$ \frac{1}{\sqrt{2\pi}} \int_{-\infty}^{\infty} e^{ipx} e^{-2x} f(x) \, dx = \int_{-\infty}^{\infty} e^{i(p+2i)x} f(x) \, dx = g(p+2i). $$ With this ODE is transformed into $$ -p^2 g(p) + b^2 g(p+2i) - a^2 g(p) = 0 $$ or more concisely $$ g(p+2i) = \frac{p^2 + a^2}{b^2} g(p). $$ This recurrence can be solved with a little guidance from Mathematica. Letting $g(p) = h\left(\frac{p}{2i}\right)$ and $a = 2c$, the recurrence for $g$ implies the following for $h$: $$ h(z+1) = 4 \frac{c^2-z^2}{b^2} h(z) $$ Assuming separability of $h(z) = h_1(z) h_2(z) h_3(z)$ where each satisfies a recurrence $h_1(z+1) = \frac{4}{b^2} h_1(z)$, $h_2(z+1) = (c+z) h_2(z)$, and $h_3(z+1) = (c-z) h_3(z)$, each of these has the solution, for non-negative $z$ and $c$ and sufficiently large $z$ (i.e. $z\geq c+1$), $$ h_1(z+1) \propto \left( \frac{4}{b^2} \right)^z \\ h_2(z+1) \propto (z+c-1)! \\ h_3(z+1) \propto (-1)^z (z-c-1)! $$ or for non-positive integral $z$ and $c$ the alternate possibilities $$ h_2(z+1) \propto (-1)^z \frac{1}{(-c-z)!}, \quad h_3(z+1) \propto \frac{1}{(c-z)!} $$ This implies that there is no unique solution to this recurrence relation. Though technically this gives two possible solutions for integral ranges of $z$ and $c$, one using the first pair of $h_{2,3}$ solutions and the second using the second pair, the possible forms for $h_2$ and $h_3$ can be mixed and matched to still yield an expression that formally satisfies the recurrence. Any resulting such expression can be analytically continued to the complex plane. Edit: the possibilities for $h_{2,3}$, including a term $(-1)^z$ that alternates in sign across the integers, are somewhat anomalous and have less natural or unique analytic continuations to the plane.
As an example, take the very non-arbitrary choice of the first $h_2$ solution and second $h_3$ solution: $$ h(z) \propto \left( \frac{4}{b^2} \right)^z \frac{\Gamma(c+z)}{\Gamma(c-z+1)} $$ and hence $$ g(p) \propto \left(\frac{b}{2} \right)^{ip} \frac{\Gamma\left(\frac{a-ip}{2}\right)}{\Gamma\left(1+\frac{a+ip}{2}\right)} $$ The proportionality factor can be fixed using the fact that $g(0) = \frac{1}{\sqrt{2\pi}} \int_{-\infty}^{\infty} J_a(be^{-x})\, dx = \int_0^{\infty} \frac{J_a(u)}{u} \, du$. This is independent of $b$ and equal to $\frac{1}{a\sqrt{2\pi}}$, yielding the final result $$ g(p) = \frac{1}{2\sqrt{2\pi}} \left(\frac{b}{2} \right)^{ip} \frac{\Gamma\left(\frac{a-ip}{2}\right)}{\Gamma\left(1+\frac{a+ip}{2}\right)} $$
Note that this is identical to the OP's proposed solution up to the substitution $p \mapsto -p$; see below comment on whether there is a possible sign disagreement. This result also satisfies the cross check that the $L^2$ norm of $g(p)$ seems to equal to that of $f(x)$, based on some numerical integrals for a few different choices of $a$ and $b$.
However, a few major limitations are that