I'm unable to check the video right away, but I'll try to quickly answer your questions.
afcraig2010 wrote:1) When I lean until the engine runs rough, it won't run rough until it's about 100RPM shy of the cruise setting I had it at. (I think that's because the sim fuel injectors have a more even distribution than they would in real life. Maybe?) When it does run rough, and then slightly push it in (so about 50RPM shy ish) that's about peak. My first question is, if I continue to lean, the RPM goes down and so does the EGT. Is this lean of peak? Or just the EGT going back down since the engine is producing less power, RPM?
The peak EGT in practice typically refers to the highest EGT value you can achieve
by moving only the mixture control. Of course, if I would find the peak for instance, and then push in some power, the EGTs may still rise (or drop, depending), kind of redefining the peak EGT. The current leaning simulation is a bit interesting in that it allows for rather lean mixtures, well lean of peak in fuel-injected engines, to run very smooth but it will still start to sputter eventually. I'd figure if the engine has a good-enough mixture distribution to run as lean as these do, it would quite smoothly lose power and eventually, maybe with just a hint of some roughness over transition, flame out if leaned far enough.
afcraig2010 wrote:2) When I lean using the method above, am I supposed to add throttle to make up for that approx 100RPM drop? 2.1) When I do that, the EGT goes down slightly (rich of peak) where I don't want it.
As before, the peak EGT is determined by the mixture control alone. If you move the other control(s), you would find the peak again, as it is "redefined" with the power setting. Typically I don't think you would add throttle to recover the lost power, but set the other controls first and then lean. Not sure about particular pilot techniques in this one - of course, you
can do that, just if the engine reaches higher power setting with your new mixture. However, note that quite often you are already at full throttle when cruising a naturally aspirated airplane.
afcraig2010 wrote:-I guess a question to pull from this is, how do they get their fuel flows for the cruise performance chart? Do they lean to peak EGT? Or to that point and then rich again a bit?
It varies quite a bit, typically it says something like "economy lean mixture" in the chart information, and then you would need to check out the specific airplane's handbook method for finding that - and to hope they are consistent with each other!
afcraig2010 wrote:4) What gauge to trust more? Fuel flow or EGT? I side with fuel flow because I've been told that the meter for it is just a gear spinning and measuring the flow (obviously) whereas the EGT is only connected to one cylinder, but I guess it would at least be accurate for that one cylinder. And is the fuel flow gauge in the 172R as reliable as the one in the Comanche? Does fuel injected vs carbureted matter for that question?
Well, EGT is highly reliable in finding the peak EGT, but it won't necessarily/typically give you that good absolute figures. Of course, the absolute figures are not that often needed, unless in some cases when going turbocharged. The "spinning-gear" type of flow meter is quite accurate, just if the indicator itself is calibrated properly. You find those in carburetted airplanes (when equipped with a fuel flow - often they are not), because they use quite low fuel pressures not allowing for the method commonly used with fuel injection, and in higher-end installations because they are, again, quite accurate. In fuel-injected airplanes one most typically finds a pressure-based indicator, calibrated to display a flow, as a factory installation. They rely on that the pressure in the line increases if a larger flow is forced into the same lines and injectors. They
can be accurate too, but are more easily affected by various factors, for instance, an obstructed fuel injector will significantly rise your fuel flow indication. Note that any issue downstream will inherently cause them to err into the wrong direction: cut a line completely, and the pressure would drop - the indicator drops too even while the fuel is in reality streaming out from the cut line.
-Esa
Maybe we should start an aviation philosophy corner as an own topic?
Speaking of mixtures and leaning, I have a (maybe) stupid question. Why can I hop in a 1941 Spitfire and set my mixture control to auto rich or auto lean and I can't do the same thing in a 1960 Comanche? 
Òûðôøüøр Ûõòúþò / Vladimir Levkov
Someone I once knew who teached both technical stuff but occasionally flying things too joked how he was annoyed by the students asking this kind of questions - making topics of the lessons look stupid, and the teachers even more because they couldn't definitely answer those! 
) but Mike Busch does give his perspective on the 'gadgetry distraction' thing 