OK, let's see...
As per the Boltzmann constant, for every 1K increase in temp, a certain % will go towards increasing the KE of the molecules and the rest to increasing PE?
No, it will virtually all go to increasing KE. Translational and rotational energies are purely kinetic (to a first approximation, ignoring intermolecular forces and centrifugal distortion). Vibrational energy is a combination of KE and PE, but for most molecules at ambient temperatures the population of vibrational states above the ground state is very small, and changes little with temperature. (So much for gases; it's a bit more complicated for liquids and solids where intermolecular/ionic forces are stronger and translational and rotational motions can be more like vibrations because there are potential energy barriers. But that's the general picture.)
What is misleading/confusing I find is that a lot of texts refer to the importance of increasing KE in overcoming the EA barrier but it seems to me that increasing PE carries a lot more importance, as demonstrated by its y-axis presence on many energy diagrams?
Suppose you are rolling a ball up a slope. It doesn't quite get to the top, so next time you roll it harder. Or you fire a rocket into space, to escape the Earth's gravity. What you are doing each time is putting KE into something in order to overcome a PE barrier. As it rises through the gravitational field, KE is converted to PE. Would it make sense to say "You're doing it wrong; you're increasing the KE, but you should be increasing the PE, because it's a PE barrier you have to cross"? How would you even add PE other than by adding KE? (Well, you could lift the ball up the slope, but not the rocket!) Similarly with a reaction - how would you increase the PE other than by increasing KE? There
are ways of injecting PE - e.g. you can tune a laser to add vibrational energy to a specific bond - but these are rather exceptional, and you are talking about ordinary thermal reactions. The energy to overcome the PE barrier comes from KE.
Due to the lower relative levels of PE, there is a flow of heat energy from the kinetic aspect of the molecule to the potential aspect thus causing the temp drop
I'm not sure what you mean here. Why should energy "flow" from kinetic to potential? Systems naturally tend to go to a minimum of potential energy, converting the PE to KE, either of an object or of its molecules (= thermal energy). A ball will roll down a slope, not up.
The small fraction of molecules that do have sufficient overall energy to overcome the EA go on to react which releases heat energy this energy is further absorbed and stored as PE.
Reaction, after overcoming the E
a barrier, means coming down the PE curve on the other side, i.e. PE being converted to KE (heat energy), not the other way round. It is
not "further absorbed and stored as PE". Note that the
overall release or absorption of heat energy in a reaction is the result of the difference in PE between products and reactants, i.e. ΔH, and is not related to E
a. That is because you put in E
af and recover E
ab, and the energy change is the difference between them, ΔH, irrespective of the height of the barrier.
As these reactions occur the larger fraction that did not have sufficient energy to overcome the EA effectively now represent an even larger % of the total molecules, and so the temperature drops further due to the absence of the higher energy molecules?
Yes, if the system is isolated from the surroundings, or heat transfer is slow. If it is in thermal equilibrium with the surroundings, the temperature will stay constant and collisions will result in the Boltzmann equilibrium being maintained, so there will always be a fraction of the molecules with energy over E
a. Even in the former case, it is not strictly correct to say that T drops "further", because depletion of the most energetic reactant molecules creates product molecules more energetic than the thermal average, but collisions will quickly even things out, so that a new equilibrium is established at a lower temperature determined solely by ΔH. (The case of evaporation referred to above is different because the energetic molecules escape from the system.)