I've managed to beat Nightmare mode, and this is my guide on how to do it. This was the way I did it and it worked wonders for me.

Note: Every time you see any yellow crates when driving the train, always get out to collect the scrap, most of the time I've collected scrap from them, I've gotten 4-5, but in my experience they can give anywhere from 1-6 scrap. This will help you in your run.

This is the link to the highligt part of my stream, this is the entire run I had, when I completed the Nightmare mode.
https://www.twitch.tv/videos/1962779432

If link doesn't work, this is the full vod.
https://www.twitch.tv/videos/1962779432

Note: I do speak Danish on the stream, but you can watch to see exactly what I did, how I fought against Charles and such. Otherwise follow the guide below, it's the description of route I planned to take. During the attempt, Charles did change it a bit, because of the timings of the encounter, but it was my planned route, and the route I took on the other attempts.

1) After Charles kills Eugene, you head down to the first location marked as 1 on the map. Here you talk to Tony Tiddle that gives you the key to his barn, go there and collect all the scrap.
Invest all that scrap into speed.

2)Once you have done that, you reverse back and go to location 2 and talk to Candice that will give you the key to her house for you to collect all the scrap.

3) After this you will be heading to the 3rd location which is Lizbeth Murkwater. Start her quest, collect the scrap in her house and on the dock, then go to the island, grab the fish and there should be 1 or 2 scrap on the island. Head back, give her the fish and run back to the train. Invest scrap to get speed level 6

4) Head down to Daryl to get the lockpick, collect the 6 scrap around his place, there are 3 train wagons, all of the have 1 each, there is 1 at table in the back of his house, 1 at the campfire and 1 inside his house.
If this is done fast is enough, you should hear Charles here , at location 5 or location 6, hide as you don't want to engage him just yet.

5) Go to location 5 and talk to Helen to get the location of the first egg. Collect the scrap around her house.

6) Go to location 6 and and talk to Sgt. Flint to do his quest and get the Flamethrower (Bug spray). There is 7 scrap around his location. 1 on the path on the way to his fence entrance, marked with an X, one on the stair, on to the left of the water tower, one behind the pile of lumber at the water tower, one in the burning house, one at the outside corner of the burning house and one at the porch in Flint's House
Upgrade damage to level 5 and armor to level 4

7) Go to location 7, this is where you will collect the first egg. If you hear Charles, hide. There is scrap around this location and in the mine, collect it all. Grab the egg and head back to the train.

Once you have grabbed the first egg it is time to move to the next part.

1) Before beginning, you will most likely have to fight Charles, and I do recommend to fight Charles off, to give you some time without having to worry about him.
When you encounter Charles, fight him off with the Flamethrower and only the flamethrower. Shoot small burst towards him, it should cool down faster than you're using it, so it shouldn't overheat. If it does, prepare to get hit.
Firing only small burst should slow him down enough so he wont hit you. Although there is a change he'll still get a few hits, if you don't fire at the correct speed.

If charles get far enough away, he'll build up momentum, here you'll have to hold down the spray just for a short while, don't want it to overheat, you have to do it in order to slow him down enough. With some practice, you know how much you have to hold down for.

When you're fought him off it time to head to the next part.

2) Head to location 8 and start Theodores quest. Go do it, I recommend luring the guard to your train and kill him, that gives you the freedom to collect the scrap at the location where you find the quest item. Head back, finish the quest and collect the scrap around the area.
Upgrade to speed 7, if you got more scrap upgrade damage, but always keep 20 scrap as a backup!

3) Head to location 9, collect the nearby scrap and then run towards the docks and start Santiago's quest. Collect the nearby scrap at the docks and in the house and run back to the train.

4) Head to location 10, collect the nearby scrap, Talk to John Smith to start his quest and go do it. You can skip it cause you aren't going to use the Rocket Launcher, but I always do it to get the scrap at the location.

5) Go to location 11, collect the nearby scrap and talk to Greg to get the location for the second egg.

6) Run to the lighthouse which is location 11, Talk to Claire to start the quest and go do it. Collect the nearby scrap and head back to the train.

If you hear Charles at any point, hide till he leaves.

7) Go to the location marked as X, leave your train here and run to location 13 to get the Journal for Santiago, collect the nearby scrap and run back to the train to continue.

Upgrade armor to 5 and then focus on damage. Now we want to max damage.

Now we are getting to the final part.
Unfortunately Steam didn't allow me to upload the picture I had of the last part of the map, no matter what I did, Steam complained about it being too large...

1) Head to the location where you get the second egg and go get it. Collect all the scrap you can find.

2) Go talk to Paul (Next blue NPC icon) and go place the explosive on the bridge. As always go collect the scrap. Finish the quest and he will give you the location for the Temple. This is where you will start the final fight vs Charles.

3) You can skip the weapon mission (Red NPC icon), as you wont use it.

4) Go talk to Gale, the last blue NPC icon, he will give you the location for the 3rd egg.

Once this is done, you have a few options.
If you feel like you have enough scrap, enough train upgrades, you can go for the 3rd egg and go to the temple, otherwise drive south to the next optional quest, drive down to the pickle lady to do her quest, and go back to give Santiago his journal. This will give you more than enough scrap to have 7 speed, max damage and 7-8 armor and gives you enough spare scrap to fight Charles when you encounter him and during his final fight.

I recommend having at least 40 scrap before going to the temple. At the final fight, Charles will go berzerk and be able to teleport around, and you will take quite a bit of damage. I used around 40 scrap during this fight and had a total of around 51 scrap.