I actually haven't got to this step in my own mod, but I took a quick try and had some success, so hopefully I will explain it correctly here if you haven't figured it out already...
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1. How do you set up so the leveled actor (giant M you place in the map) will spawn different difficulties of enemies depending on the players level?Those 'M's come from creatures or NPCs with ActorBase's set under the template (if you open up a creature and look left bottom side there is a 'Template Data' section). To spawn enemies based on the players level, there are a couple ways I imagine you could do it.
Perhaps the simplest, but less defined, way of doing it is to create a new supermutant creature with his level modified based on the players. Under the Stats tab you would check PC Level Mult, then it could be based on Player level.
How they tend to do it, though, relies on using the Ms by setting up the template data. In this way you will be using a leveled creature list to select mutants you want. Again, I think you can use the PC Level Mult option, but they tend to use a variety of creature templates. So, you might make several custom mutant templates. For instance CrMyMutant1 would be a super mutant level 1, perhaps using his fists. CrMyMutant5 might be a level 5 with a nail board. CrMyMutant10, level 10 with a sledge. CrMyMutant15, level 15, with a supersledge.
These are all just examples. You can set the custom creatures however you want, adding special perks, stats, etc. based on which level they are. Then you create a leveled list (under Leveled Creatures; say myMutantLvlList), and in it add each of the versions of the mutant you created (CrMyMutant1,5,10,15 in our example). On the right you can select which level the PC has to be for those monsters to appear. For instance, you could set CrMyMutant1 to level 1, CrMyMutant5 to level 5.
Of course, if you want the area to be tougher, you can allow the monsters earlier. Perhaps if the PC is level 3, then level 1 or 5 mutants could appear. Likewise, if you want to make it easier, maybe CrMyMutant15 will only appear if the PC is level 20 or more. You could also make them all only require level 1 from the PC, allowing ANY of them to spawn right from the get go.
If you want it to be varied, you can select "Calculate from all levels <= PC's level". This makes it so the M could spawn ANY of the monsters in the list, so long as the PC level is greater or equal to the required one. In our example, if we had each mutant version appearing at their level (ie, CrMyMutant 5 at PC level 5), then having the option check would allow EITHER a level 1 or level 5 mutant to appear. The count is generally left at 1. If you want multiple monsters to appear, simply lay down more of the spawners.
Speaking of which, onto how to actually create the "M". Oddly enough, you use another creature (you can't lay down the leveled list itself). Create a new creature (say, LvlMyMutant). Under template data, select the actor base and scroll down to the leveled list (in our example, myMutantLvlList). Then check the desired boxes in the template data section. In this particular case, you can likely select them all. This way, you won't have to change any of the information - it will simply use those from the leveled list, which in turn draws from each individual mutant you created.
Now slap down the new creature (LvlMyMutant), and viola! A nice little M of your own to put down. If you want several to spawn, place multiple Ms where desired.
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2. How can I set it up so each enemy will get one of 2 or 3 weapons (depending on the players level, and the strength of the enemy)I guess it depends how you want to do it. If you were following the example prior, then you can do it simply by giving each version of the mutant a particular weapon. As I gave an example, it could be Lvl 1 has no weapon, 5 has a nail board, 10 has a sledge, and 15 has a super sledge. Then, depending how you set up the leveled list it would already be done.
As a thorough example, if you set it up as above, and the PC was level 8, let's look at a few outcomes depending on the leveled list if we had 4 individual spawners.
If each creature appearing only when the PC was equal to their level, and only the highest creature appearing...
There would be 4 level 5 monsters with nail boards. The PC wouldn't be high enough to spawn the lvl 10 ones.
If each creature appearing only when the PC was equal to their level, and any creatures lower and up to the PC could appear...
There would be 4 monsters, each being either level 1 or 5 randomly, with their appropriate weapons. Again, the PC couldn't spawn lvl 10 creatures, but could spawn either 1 or 5.
If each creature appearing at any time, regardless of PC level...
It would be utterly random. There could be 4 level 15's, 2 level 10's and 2 level 5's, or any other combination of 4 creatures.
As you can see, simply altering the leveled list (creating multiple ones if you need to - just remember to create separate creatures to make use of the new lists) can change it as you need.
Besides that, you might be able to set up a leveled list of items, adding in each weapon. For instance, you might make a list called NailboardSledge, which contains a nail board and a sledgehammer. Throw that on the inventory of the CrMyMutant10, and suddenly he could spawn with either a nail board OR a sledge.
Speaking of, if you noticed the "WeaponList" option under the creature, this is a set of restrictions that the creature can use. For the Super Mutants, it will probably be fine to leave it as default Super Mutants the way you described it. If you want to change it, however, you must use form lists. To do so, go to the form lists, and create a new one (say, MyMutantWeaponForm). Then, simply drag and drop the weapons from Items->Weapons into the form. Now, go back to the creature and change the weaponlist to the newly created form, and the mutant will only be allowed to equip and use those particular weapons.
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3. How would I make the enemies randomly have somewhere from like 0-50 of a custom ammo type I made?Easiest way I can think is to create two new leveled lists (Leveled Items). First, create your new ammo type. Base it off an existing one or however you want it made. Now, create a leveled list ( should probably name it more appropriately to your own ammo and the values set inside the list). Put in a single count of the ammunition. Set a chance for none. You can tweak this as you see fit. The game tends to use 25, 50, or 75 I think, but you can set it however you want. The higher chance there is for none, the more likely you are to get less ammo.
Now, create another leveled list. In this one, you are actually going to use your previously created list as an item. Set its count as you see fit (for example, 50). You don't need to change the chance for none, as the previous list will still use its own (unless you want to have a chance no ammo will appear at all regardless of the previous list).
Let's assume you put 50 chance of none in the first list. Now with the second list, it will basically run through 50 times (the count of the second list), and each time it goes through there will be a 50% chance of adding 1 ammo or 0. Now obviously doing it this way, there will be only a tiny chance of getting 0 ammo or 50 - it would have to have the same outcome 50 times in a row.
You can of course tweak the % chance of none, as well as using multiple lists in the second one. For instance, you might create a list with 75% chance of none, one with 50%, and one with 25%. Then put all three of these lists, with whatever counts you see fit, into a single list. That will change the odds depending on each individual list (be sure to check Use All in the list if you want it to draw from all of those lists).
Kind of a rough explanation, but if you need to see how they did it, you could check under containers for the ammo boxes and keep double clicking each list to see how they set it up in game.
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The main thing I dont really get are leveled lists, formlists and those kinds of things. In an earlier spot in my mod, I have enemies set up with a leveled item list in their inventory. If the player is below Lvl 8 it gives them sledge hammers, if 8 or above, supersledge. But somehow those mutants always spawn with either nothing, or grenades...Hmm, it would depend on which one you used to see what exactly went wrong. It could be an 'ondeath' item set, a leveled item list in their inventory you left that is giving them the possibility of grenades, etc. I never got a chance to mess around with using lists at particular levels (such as 8 below or 8 and above), and probably won't have time right now (this post is longer than I thought =D). I only looked at an example or two in game, but they seemed to just have equal chance of using a selection of items regardless of level, then each individual template had a selection. So you might make one low level monster that can only get nothing or a nail board (use %chance for none in list), while a higher level will have either a nail board or a sledge (regardless of level). Or set it so that higher level creatures ALWAYS have the higher level weapons. Then you can use the leveled creature list to determine when those particular monsters would appear (that way low level PCs would never see the higher level monsters with the higher weapons anyhow).
I realize this is a lot of info, and probably overly wordy. Hopefully it points you in the right direction to start. Like I said I don't have any real experience myself with this, but I did create a test mod and it seemed to work fine. I was getting variable bits of new ammo (usually around 25 for the simple 50% chance I used), and I had monsters spawning at or below my level (my own example had weak, normal, strong mutants; mixed groups spawned as I was higher levels, only weak when I was low, etc.).
If you need help on something in particular or need me to explain differently something let me know.