good job for getting some of the basics out of the way.

seems like people skip all of that and still want someone to diagnose their problems.

What kind of car is it?

bogging down like that can be caused by a few different things.
I would start with the coolant temp sensor. When that sensor goes, the ECU will do all kinds of stupid stuff.
From there, I would want to know what the fuel pressure is. If the fuel pump is stock and has a ton of miles on it, then it is possible that it is taking a crap on you, not getting enough fuel to the rail and the ECU is pulling crazy timing trying to keep itself alive until the fuel can catch up.

It doesn't sound like you are loosing spark because that would be far more rough. And it would be very rare for it to be all cylinders at the same time. If it was the coil, the coil would get hot, the resistance would get too high, and it would drop spark all together until it cooled off. But since you say it eventually catches up with itself, I wouldn't think it is a spark issue.
As for the cam position sensor, those do go bad. But again, that is one of those things that is pretty much good, or not. They do the same thing as the coil. Once they get too hot, they stop working, and the ECU kills the engine and it won't start until it feels like it.

When the EGR is the issue, it is typically at highway speeds. Or cruising with really light load, and it is usually just a vacuum leak when the valve opens. Or it gets stuck open and it can make it tough to start and run like balls because the ECU doesn't know it is open so it just sees a massive vacuum leak.

I would start at the coolant temp sensor. Then Fuel pressure. I would also want to know that the injectors are in good shape. An Ohm test can tell you if they are good or not. I personally would want to pull the fuel rail and actually see the injectors spraying to see how the fuel comes out. Can also help tell you if any of them are leaking or anything like that. I would also check the throttle position sensor to make sure it is reading correctly. (pretty much all of this can be tested with a multi-meter)

somewhere in there, you should uncover your issue.
If not, then I would start thinking about taking it to a shop.
I just wouldn't want to pay a shop 75 buck (or more) an hour to do stuff that I could do myself in an afternoon.