So I noticed the alignment specs don't mention how high the rear should be. I've heard it's a good rule of thumb to have the rear be half an inch higher than the front but i'll be measuring from the pinch welds. What's the best way to go about measuring this?

Read the alignment specs again. Specifically the sections about rake.

Oh wow, now I see it. :facepalm:

So I spent a good amount of time adjusting the ride height of my car, after going on a somewhat aggressive drive they dropped a bit. Around 1/8th of an inch on each corner. My question is, how many miles should I put on the coilovers before I can safely say they're broke in and settled enough to not drop down after adjusting them?

The shocks do not break in or settle. That's your measuring technique. If you have OEM rubber bushings, it's tricky to get the car to fully settle in between adjustments. Have to roll it back and forth a bit. That's why we use hubstands and bounce on it.

Interesting, any idea why the height changed after driving?

He just told you. The stock rubber bushings tend to bind when you change the ride height of the car, and only by rolling the car back and forth a bit, or in your case going for a drive, do they "reset" to their neutral position. This is why you noticed a change in ride height after driving the car.

Gotcha. So now that my ride height is set-up properly I've noticed that the gaps between the tire and wheel well are different in the back. My back right wheel gap seems a bit larger than my back left wheel gap even though the measurements from the pinch welds to the group are basically identical. I'm assuming I should trust the pinch weld measurement but I'm just curious as to why the wheel gaps are different. Perhaps the fenders were rolled poorly?

We have not measured fender height on any car in our shop in probably half a decade.

Okay, so it's probably safe to assume my fenders are just pulled/rolled poorly?

Youre trying to measure from a piece of metal thats somewhere between 2 to 3 decades old. The ground from which youre measuring on (read: not level) could be a factor and throwing off your measurements. Or you being in/getting out of the car can also be a factor. Or fenders are misrolled.

Stop worrying about it.