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Everyone that says get to that podiatrist has got it right. I'm curious, though, except for that bruising do you have the same issues wearing regular shoes, too? If you've got a certain insole that helps with them I'd swap them into a lower boot and see how it feels.

BTW, having thought about this and the illustrations etc about Mortons' whatever over night... I believe your entire problem could be the Mortons' whatever... The nerve in question at one point passes through the region of the ankle (it has to, in order to reach the foot) and then lower in the foot branches out and serves the region of the ball of the foot. The point is, you *have* the symptoms of the known issue and it involves impingment of the nerve in the ankle area. That explains the sharp pain under the ankle bone and the other pain (apparent bruising pains) in that area. And the apparent/symptomatic pain in the ball of your foot could actually be from the nerve impingement in the ankle area causing the nerve to generate pain signals that your mind associates with the ball of your foot. In my mind this is similar to how wacking the "funny bone" in the elbow can cause odd sensations across the entire lower arm. Or how sciatic nerve impingement in the lower spine can cause symptomatic pain in an entire leg. All that being the said, I *strongly* advise you to visit a podiatrist. Nerve impingement can lead to nerve damage and chronic pain/nerve/function issues. This is not something to be trifled with...

[ Odd, I just posted this answer and it appears to have fallen into the bit bucket, so I'm trying again. Apologies if it ends up posted multiple times... ]

I used to sell footwear…

First, I don’t believe you are doing anything wrong.

Feet come in nearly infinite variety, footwear does not. The result is some people (lots of people, actually) experience at least some pain (more generally, discomfort…) and/or have trouble finding footwear of specific types that fit well to be serviceable. You are not alone…

That being said, pains like you describe can be caused by a nearly infinite range of problems, so it's difficult to diagnose sight-unseen.

However, given that your problem is partially debilitating, that it (apparently) involves nerve impingement (which could result in chronic problems), and that it is happening with more than one pair of footwear…

My recommendation would be to take yourself and the boots to a podiatrist who entertains/deals-with sports-related problems and start there.

Given that you have one or more foot/fit problems already, I do not necessarily believe that lighter/softer/cushier footwear will necessarily fix the problem(s.)

If you are carrying more than casual daypack (ultralight backpacking) loads and/or if you have less-than strong ankles and/or if you are hiking on uneven or rocky trails (or backcountry/off-trail), you might well end up with just as serious problems in terms of ankle support, rock/stone bruises, and more generally beat-up sore aching feet or twisted etc ankles.

And in the end (given that you have a pre-existing condition) you might actually require more support (or support of some different kind altogether) rather than less…

Again, if I were in your shoes (pun intended) I’d start with a good sports-oriented podiatrist or other foot specialist...

Wow, this is tough. Brian below is on to something; whether it's a really great footwear specialist or a doctor. Orthotics can make a huge difference! I think the other thing to think about is whether or not boots are necessary.  If you are only using a light pack and doing day hikes, plenty of my friends just hike in trail runners, which offer great traction. Let us know how it goes, we want you out hiking too!

How are you buying boots? Are you going to a reputable outdoors store with experienced boot fitters?  If not that is what you should do. Otherwise you are just shooting in the dark.  If as you say, you have specific issues with your feet it may also be a good idea to visit a podiatrist and get custom footbeds.