Hello Kevin,
So, given that all of your lab work and blood work has been normal, I think you're experiencing MILD exercise-induced rhabdomyolysis. There's a paper on it at the following link:
http://www.charlydmiller.com/LIB04/1994exerciserhabdo.html
To summarize, basically, there has been this theory that strenuous exercise can cause some muscle breakdown, and that that manifests itself in your urine. Your urine will change color, but it's not actually BLOOD that's the color change; it's actually a byproduct of muscle breakdown. In fact, we KNOW this happens. Weight lifters, for instance, may well have elevated levels of this byproduct (called myoglobin) in their urine, and their blood may show increased levels of creatine phosphokinase, or CPK. Again, this isn't exactly a bad thing; the whole POINT of strenuous workouts (especially weight lifting ones) is to break down some of the muscles, so that when they regenerate, they are hypertrophied, and therefore bigger and stronger, compared to before.
So the authors of this article took a population of men who happened to be in prison, and who were all exercising, and would complain of arm or leg pain. I'm SURE you've probably felt some pain in the course of your workouts (as have I)... they then did two measurements: they measured their CPK in the blood, and looked at their urine. ALL of the men had elevated CPK, and all of them had myoglobin (which "looks" like blood) in their urine... however, none of the men developed renal failure, or had any other negative consequences for their symptoms. And that's also a good thing. See, it had ALSO been thought that rhabdomyolysis caused by exercise MIGHT lead to kidney failure, and that would be bad... but this study suggests that's not the case.
HOWEVER, there are other studies out there that suggest that you CAN develop acute kidney failure as a result of this. Now, the way you're describing your symptoms, it SOUNDS like you aren't getting anywhere near to that point. People that have exercise-induced rhabdomyolysis that requires them to be in the hospital usually have much darker urine than what you are describing.
Basically, the way to prevent, or make it better, is simply to be better hydrated. Like, aggressively hydrate yourself. Which I imagine you do, anyhow, because if you're running 40-60 miles a week, you HAVE to.
I mean, consider this. There are hundreds of thousands of people out there running marathons, lifting weights, and being in good physical condition and the vast vast majority of them do not develop kidney failure, or really severe rhabdomyolysis. Do many of us probably pee out some myoglobin after (or during) a hard workout? I'm SURE we do. And we may not be paying much attention to our pee... or we're drinking so much fluids that we can't see the color in our urine anyways, even though it may be there.
So, for you, I'd say, be more aggressive with hydration.
Now, is there a connection with either the aspirin, or the advil? Perhaps. As you know, both drugs affect your platelets and ability to clot, and in fact, both also affect your kidneys. However, the effects of aspirin on your blood can last 3-5 days, while advil does NOT have this same effect... when advil is gone out of your system after a few hours, it's gone. So, I might suggest that you avoid aspirin and try advil for your headaches. Or Aleve. Or tylenol. Or even a combination of tylenol and advil (ie, take 500 mg tylenol AND 400 mg ibuprofen at the same time). See if that helps.
Let me know if you have any questions about all of this.
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