I shall attempt to induce an intuitive grasp of the matter here, not strive for exact representation of the physics involved:
do the electrons of one molecule get kicked up in a collision and emit a photon?
There is no "collision" per se, just a change in exactly how the electrons are delocalized around the nuclei. The term you are looking for is
spontaneous emission.
If we consider a single molecule that does not interact with others, its velocity does not necessarily reflect its temperature. If that molecule is "hot", it means its internal degrees of freedom -- positions of the atoms in the molecule in relation to each other, the "electron cloud" around the nuclei -- contain "extra" energy; i.e., it is in an excited state, vibrating and whatnot. This energy, no matter how low, can be emitted as photons via spontaneous emission. It is a quantum mechanical phenomenon.
If we consider a gas, liquid, or a solid, then the velocity of the molecules are involved in the temperature, because the molecules will collide with each other; the thermal energy will relatively quickly reach an equilibrium where some of it is in the velocity, some in the internal degrees of freedom. Again, the excited internal states can drop to lower energy states by emitting a thermal photon spontaneously. In the next few collisions with other molecules, the internal degrees of freedom will accrue more of the left-over energy, and the molecule slow down. (Conversely, if the internal degrees of freedom gain energy from photons, in the next few collisions the molecule will speed up.)
(In magnetic fields, the interaction between the electrons and the field exerts "pressure" on the entire molecule, so the molecule can slow down via photon emission even without collisions. Similarly, at very low temperatures, laser light (photons with the same energy and phase) can actually keep atoms in place without heating them up; these are called
optical tweezers.)
Note that even intergalactic space isn't really empty enough to allow many molecules to zip along at huge velocities, while their internal structure is at or near a ground state: there are photons everywhere (microwave background at minimum), magnetic fields, and even an occasional atom or molecule here and there.
how does this process work in the accretions disk of super massive black holes with xrays
At highly energetic environments, the electrons around nuclei get so big energy kicks that they fly off completely. You get plasma: atomic nuclei and electron soup. No molecules. No spontaneous emission from molecules, because there are no intact molecules.
Instead, you get stuff like
brehmsstrahlung or "braking radiation", electromagnetic radiation produced by the deceleration of charged particles.
(Edited to add: If you want to generate x-rays, just peel off Scotch tape off its reel.)
My understanding is that only electrons changing energy state can radiate photons.
No, there are a few other ways (than electron dropping to a lower energy state when bound to an atom, molecule, or lattice), like
phonon energy state changes, too.
On the opposite end how does a long metallic wire emit a photon on an antenna at say 1000 meters in the (300)khz bands? One atom can't make anything that large.
In metals, some of the outer electrons are not bound to any specific atom, but to the entire lattice. It is these electrons that interact with those photons.
Or can super high energy collations generate gluons or weak bosons?
When you get to sufficiently high temperatures and pressures, even atomic nuclei break down into quark-gluon plasma. So, a single collision is unlikely to suffice; you need a lot of them in a small volume in a short timeframe to get to that.