I understand that the integration by parts that I posted is a very naive attempt at following the statement by Jackson that the result can be obtained by an integration by parts. Using your suggestion of ##\Phi \nabla^2 \Phi = \nabla \cdot (\Phi \nabla \Phi) - |\nabla \Phi|^2## is very straightforward and economic:
$$
\int_V \Phi\nabla^2\Phi d^3x=\int_V \nabla(\Phi\nabla\Phi)d^3-\int_V |\nabla\Phi|^2d^3x
$$
By the Divergence Theorem
$$
\int_V \nabla\cdot(\Phi \nabla \Phi)d^3x=\oint_S\Phi\nabla\Phi\cdot \mathbf n da=\oint_S\Phi \frac{\partial \Phi}{\partial n}da
$$
Now, the integration is over all space and then the surface S goes to infinity and so the surface integral vanishes, leaving
$$
\int_V \Phi\nabla^2\Phi d^3x=-\int_V |\nabla\Phi|^2d^3x
$$
But I wanted to follow Jackson when he states that the result can be obtained by an integration by parts. This can be done by decomposing the vector in its components
$$
\int \Phi\nabla^2\Phi d^3x=\int\Phi\left(\frac{\partial^2 \Phi}{\partial x^2_1}+\frac{\partial^2 \Phi}{\partial x^2_2}+\frac{\partial^2 \Phi}{\partial x^2_3}\right)d^3x=\int\Phi\frac{\partial^2 \Phi}{\partial x^2_1}d^3x+\int\Phi\frac{\partial^2 \Phi}{\partial x^2_2}d^3x+\int\Phi\frac{\partial^2 \Phi}{\partial x^2_3}d^3x
$$
Now, integrating by parts
$$
u_i=\Phi,~du_i=d_i\Phi=\frac{\partial \Phi}{\partial x_i}dx_i\\
d_iv=\nabla^2_i\Phi dx_i=\frac{\partial^2\Phi}{\partial x^2_i}dx_i=\frac{\partial}{x_i}\left(\frac{\partial \Phi}{\partial x_i}\right)dx_i,~v_i=\frac{\partial\Phi}{\partial x_i}\\
\int\Phi\frac{\partial^2 \Phi}{\partial x^2_i}dx_i=\Phi\frac{\partial \Phi}{\partial x_i}-\int\frac{\partial\Phi}{\partial x_i}\frac{\partial\Phi}{\partial x_i}dx_i=
\Phi\frac{\partial \Phi}{\partial x_i}-\int\left(\frac{\partial \Phi}{\partial x_i}\right)^2dx_i
$$
Now
$$
\int dx_j\int dx_k\left[\phi\frac{\partial\Phi}{\partial x_i}-\int\left(\frac{\partial\Phi}{\partial x_i}\right)^2 dx_i\right]=\int\Phi\frac{\partial\Phi}{\partial x_i}dx_j dx_k-\int\left(\frac{\partial\Phi}{\partial x_i}\right)^2 d^3x\\
$$
and
$$
\int \Phi\nabla^2\Phi d^3x=\int\Phi\frac{\partial\Phi}{\partial x_1}dx_2 dx_3+\int\Phi\frac{\partial\Phi}{\partial x_2}dx_1 dx_3+\int\Phi\frac{\partial\Phi}{\partial x_3}dx_1 dx_2-\int\left[\left(\frac{\partial\Phi}{\partial x_1}\right)^2+\left(\frac{\partial\Phi}{\partial x_2}\right)^2+\left(\frac{\partial\Phi}{\partial x_3}\right)^2\right]d^3x
$$
From Green's First Identity it can be seen that
$$
\int\Phi\frac{\partial\Phi}{\partial x_1}dx_2 dx_3+\int\Phi\frac{\partial\Phi}{\partial x_2}dx_1 dx_3+\int\Phi\frac{\partial\Phi}{\partial x_3}dx_1 dx_2=\oint_S\Phi\frac{\partial\Phi}{\partial n}da
$$
and we have
$$
\int\left[\left(\frac{\partial\Phi}{\partial x_1}\right)^2+\left(\frac{\partial\Phi}{\partial x_2}\right)^2+\left(\frac{\partial\Phi}{\partial x_3}\right)^2\right]d^3x=\int|\nabla\Phi|^2d^3x
$$
and then
$$
\int \Phi\nabla^2\Phi d^3x=\oint_S\Phi\frac{\partial\Phi}{\partial n}da-\int|\nabla\Phi|^2d^3x
$$
Now, again for the same argument, the integration is over all space and then the surface S goes to infinity and so the surface integral vanishes, leaving
$$
\int \Phi\nabla^2\Phi d^3x=-\int|\nabla\Phi|^2d^3x
$$
the same result as using ##\Phi \nabla^2 \Phi = \nabla \cdot (\Phi \nabla \Phi) - |\nabla \Phi|^2##, but way lengthier.
I value a book by the way the author induces us to work out tools and techniques to solve problems, that's why I wanted to see an easy way to perform the integration by parts in the vector integral equation. But vector calculus isn't as straightforward as single variable calculus as we must deal with the components and the scalar and cross products. I really wished that there were an easy way to perform the integration by parts in vector calculus. It would be a technique worthy of keeping in memory.