Hello Nick
The reduce.out output shows a decent convergence behaviour.
EPS_SCF at 1E-3 is definitely too low and the forces are going to be wrong.
The cutoff at 300 Ry is too low and it is also going to affect the accuracy of the forces.
Not accurate forces might explain the high temperature and for sure lead to wrong dynamics.
If the temperature is very high, or anyway with large velocities, it is a good idea to use a variable time step, to avoid too large displacements.
Check the DISPLACEMENT_TOL keyword in the MD section.
Have you tested AIMD on your system without the modification of the velocities to induce the collision?
Regards
Marcella