Alright, time for the dangerous stuff, ignition settings:
This can be really simple and really complicated both, depending on your setup and what development has already been done by Megasquirt users. In the case of my 2006 5.7, it's pretty straightforward. The main things you set up in this initial window are the triggers the system will use to determine crank (and potentially cam) position. In the case of my early 5.7, the crank uses a tone/reluctor wheel with 32 teeth (though spaced in such a way that there would normally be 36 teeth). There are some missing teeth on there and there are also some "doubled" teeth (reference picture below).
This is what the 36-2+2 refers to. It's a "36" tooth ring with 2 missing teeth and two "double" teeth. You can see them on the picture above. The missing and doubled teeth are positioned at specific places on the crankshaft to help the computer know where TDC is. This actually simplifies a fair portion of the rest of the settings as those values are sort of "baked in" so they don't have to be manually set. The trigger angle setting you can follow the tooltip on. With the 36-2+2 wheel you can leave it at zero. I believe the later Hemi used a 60-2 wheel. They would likely be a similar setup, but I can't say for sure as I haven't messed with one. The tooltips do a pretty good job of walking you through and there is a good amount of info on the internet from people that have set up the MS on the later Hemis to get you going in the right direction.
The "skip pulses" setting basically just ignores the first number of pulses the sensor sees when you first crank the key. I guess the idea here is to let the sensor settle and to get clean pulses. This probably matters more if you have a VR style sensor compared to a hall effect one. Hall sensors tend to have pretty clean square wave signals while VR sensors produce more of a varying amplitude sine wave, so it might take a couple teeth going past before the signal is high enough to read on them.
Pretty much all of the settings here I got from this link:
How to MegaSquirt Your Chrysler Hemi Engine. It's a good resource and helps with these settings, though it doesn't necessarily explain the "why" on a lot of them too much, so just be aware.
I can't really speak to what the ignition input capture setting affects, other than that you're either reading the rising edge of your crank sensor signal or the falling edge. There is some note about how it could affect things on the tooltip, the primary one I could see is just that the offset you might get if you are reading on the wrong edge could very slightly affect your timing. Like if the tooth is clocked in such a way that the front of it is at TDC and you are reading the falling edge, you would in theory be some amount of degrees or fractions of a degree off of that.
The spark output setting is one of the more important ones on this page. I believe it defines more or less "how" the coils are fired. In the case of my sequential setup, I'm using the MS3X spark outputs, which are 5v logic level signals. So to fire a coil, the signal goes from low to high. If you have it backwards, the coils would stay energized most of the time instead of only during the dwell period, which would be pretty bad for them.
The number of coils setting could potentially be a little confusing if you look at the options. Wasted spark is an option, which the really early 5.7s did, but not in the way that this setting means it. "Wasted spark" here would more generally mean you have half as many coils as you have cylinders, so each coil has to run two cylinders. The early 5.7s still had 8 coils, but were just wired in such a way that they sparked two cylinders at once, so you'd still want "coil on plug" here. I think "wasted COP" just fires each coil twice (once before power stroke and once during exhaust), but I'm not actually sure. I guess you could do that, but I didn't see a reason to.
Spark hardware for me was the MS3X since I'm using those outputs to drive my coils. This comes down to how you build your board.
Cam input is where your cam sensor is wired up, fairly straightforward.
The "flip polarity" setting on the cam input I believe has to do with the way the cam trigger wheel is built. In the case of the crank trigger, the teeth are "positive" relative to the rest of the wheel. On the cam wheel for the early 5.7s at least, it's a bit different:
On these, there are windows for the different cylinder. However, that means the rest of the wheel is solid, so when the sensor is looking at it, you'd see a "high" signal most of the time and it would drop to a "low" when a window goes by. I believe that is where this inverted setting comes into play. If you had a tooth style sensor instead, you would probably leave it as normal polarity.
The values on the right side of this setting window are generally about setting up your coils. The fixed advance box can be used to force an ignition advance so you can check your settings with a timing light, though you can also sort of do that via the spark table later. "Use prediction" is actually kind of a neat setting that factors in how your engine is accelerating to the timing calculations. So if your rpms are rising really quickly, it might advance the timing just a tiny bit more to try to get the spark at the number you actually have in the table. I believe this is actually how some of the misfire monitors work on modern engines as well. Sometimes, if you put a lightweight flywheel on a car, the ECU actually sees the faster acceleration and jerk of the crank sensor between teeth and thinks there was a misfire. Just something I found interesting.
Cranking dwell and advance are just that. You can give your coils a little extra juice during cranking to get some more spark, potentially. This is kind of like how the old ballast resistors worked. During cranking you would actually feed the coil 12v for a hotter spark, but once you let off the key the signal would go back through the ballast resistor and drop the voltage so the coil wasn't worked as hard. It's probably not that important on COP setups, though I still have mine set a touch higher because I think that was the default. Dwell type we can leave at standard, this is mostly for some other spark systems and modules out there. You can also set up the dwell via a table if you wanted to change the value through varying engine conditions. Again, this is probably more useful on a single coil setup where you might have limited dwell time at higher rpms or if you needed more dwell at low rpm for idle or something like that. If you don't use a table, the next settings are the fixed dwell values you want. This is another reason I was trying to hunt down a factory tune, though in the end it didn't help. I have struggled to find any real information on the stock 5.7 coils. I know they are good and generally even regarded to be better than a lot of the aftermarket replacements, but the very limited information I ever found on them was not much help. I found one guy that was doing dwell studies on coils with a scope to show when they were hitting saturation and what kind of spark energy they provided, but for some unknown reason he was only running them at 6v or something like that, so I didn't think the information was as useful. For the time being I've stuck with the "default" value of 3ms. The spark duration value is how long it takes the spark to actually happen. You could also think of this as "coil discharge time". I believe this is used as a safeguard of sorts for high rpm situations where you might not have enough dwell time between ignition events. So in our case it could something like "I need 3ms to charge and 1ms to discharge, but I only have 3.5ms between ignition events", so it would drop the dwell time so it's not trying to charge the coil up again while it's still firing. Or at least I'm pretty sure that's how that is meant to work. For COP setups, it's probably not super important because each coil has a good amount of time between sparks, but for a single coil distributor setup it could matter more. If you run high enough rpm I guess it could matter with COP too, though I forget just how high it would have to be before you'd see any issues.
Spark hardware latency I can't really say much about other than what it sounds like. It would help account for any kind of lag you might have in the system, like maybe if you were running an MSD box using the MS as a trigger and the MSD box had some kind of delay in it you needed to account for. Or not, I really don't know enough about it.
Spark trim is a novel option, though I don't have enough sensors on my car to know if it would be useful. It basically lets you alter timing per cylinder as needed to address any issues you might have. This is usually more of a fuel problem (which you can do individual injector trims as well like if you had a lean cylinder). Spark could be used in a similar way where maybe you'd want to pull a degree or two on a leaner cylinder. The knock section later can actually do this automatically as well, though it would mean you'd have to be knocking for it to trigger vs hard coding it here if you knew you had one cylinder that was always a problem.
