I'm similar to you in that I overpronate on my right foot and am fairly neutral on my left.
I find having two pairs of shoes, one with a strongish level of support and one with a milder level of support works quite well.
The milder shoe tends to be fine for my left foot and okay for a run or two for my right and then I change to the more supportive shoes and repeat.
Bear in mind that most injuries are caused by over use, that is, repeating the same biomechanical imbalances in your body. So changing between the level of support in shoes prevents this.So does changing between a firm shoe and a soft shoe from my experience.
As achilles problems are often caused by running in soft shoes switching to the firmly cushioned Brooks may help but I would certainly recommend keeping the Nike and alternating between shoes when your injury clears up.
PS. I'm actually running in three different shoes at the moment, Brooks Adrenaline, Nike Air Structure and Mizuno Wave Inspire
Don't worry about the hydrostatic head. All waterproof jackets are waterproof enough for all practical purposes unless you plan on crawling through a bog all day long.
Secondly MVTR is only a guide and depends on humidity, temperature gradient between your inner clothing and shell, how good your DWR is on the outside of the jacket and whether it is actually raining.
For example Goretex Paclite has a high MVTR but users experience suggests it is not very breathable when it is actually raining. (much better in the dry)
And if it is really cold your condensation will freeze on the inside of the jacket as it will never be warm enough to evaporate or stay as water vapour. And none of the membrane materials like goretex and event will transmit liquid water (paramo will but works on a different principle).
As mentioned above venting options like mesh pockets, pit zips, adjustable cuffs are usually more significant from a breathability perspective. Other features to think about are good hoods with wired rim and the fit ( for tall people the length of the jacket for example). These features can affect the weight and durability (more taped seams) and often it is a trade off between weight, complexity and features
So I would choose a good quality material like event or Goretex Pro shell and then concentrate on the features you're interested in at the price you can afford.
Whether you over pronate (badly or otherwise) depends on a huge range of factors from your genetics, age, weight, any medical conditions and even things that occurred when you were younger (and body developing ).
An example is that I overpronate on my right foot and am neutral on my left foot. This is possibly due to an injury/weakness that I gained on my left ankle and 11 years of carrying school books under my right arm to and from school several times a day (you tend to lean in the opposite direction when carrying weight).
As for correcting fallen arches. I doubt that is possible but you may be able to strengthen them through exercises. Otherwise a supportive insole that fits your arch shape is recommended regardless of the shoe that you end up with. The ones supplied with the shoe are usually pretty rubbish.