Let me preface this by saying this is what I got out of it and not definitive. This is from a combination of the series and reading the manga.

[I’m also a bit confused as to what actually happened towards the end where Kuro shows up in the city before it’s destroyed, running from the red army. Was that just a random flashback to show how the city got fucked up in the first place?]

I don’t think it was a flashback, but rather a flash forward. When you see Kurou wake up, he looks upon the city that is completely rebuilt. Add to that the fact that in the following clips we get a quick glimpse of the Red Emperor (Benkei) ordering them to find and kill Kuromitsu. Now he lifts his hand up briefly and you can see just how much it has shriveled - showing that he’s aged even more after the time we see him meeting with Kuromitsu. Afterall, he gained immortality and Kurou didn’t cut his head off after their duel. I think this point is just to show that the cycle of Kurou and Kuromitsu meeting and running from their pursuers is endless.

[Also what was the point of Kuon’s body? Was it really just a replacement for Kuro’s body? If so why? Is his head the only thing that doesn’t age?]

Kuon was created specifically for Kurou - as he needs to replace his body every 100 years or so. The reason Kurou has to change bodies every 100 years is because when he drank Kuromitsu’s blood, Benkei chopped his head off before the blood could finish mixing. Kuon is actually a ‘complete’ immortal like Kuromitsu. She created him in hopes that giving Kurou an immortal body would eliminate the need for him to switch bodies. It’s not that his body doesn’t age, it’s just that it can’t take the constant damage and regeneration. After awhile it begins to weaken until he can’t move anymore.

[I can see from the very end that they did not actually “go back in time” since there was buildings destroyed all around the forest that Kuro and Benkei where in. I can only guess that this is a never ending cycle that Kuro and Kuromitsu created into order to survive and keep their relationship fresh.]

Not so much to keep their relationship fresh as it is a necessity of Kurou switching bodies. As she is being pursued, Kuromitsu can’t exactly wait around for Kurou to finish joining to his new body and she has faith in him that he’ll find her.

[Also the evil old guy was still not explained other then he wanted Kuromitsu dead…]

The ‘evil old guy’ is Benkei. He was jealous of Kurou for his relationship with Kuromitsu. He betrayed Kurou to the group that was chasing them at the time and found out that Kuromitsu is immortal. He spends the next 1000 years chasing her so that he could tell her his feelings. A little bit crazy and obsessive? Yeah, but look what she did to Koun. This is a woman who has a great power over men.

Overall, the ‘ending’ is left up for the viewer to decide. Was it a dream? Possibly, but the destroyed landscape around the jungle suggests not.

No, The thing is, Kuro’s body ages normally. The time when Benkei cut off Kuro’s head, the process of his transformation wasn’t fully done. So Kuromitsu has to get a new one about every 20 years. When she chopes off Kuro’s head and attaches it to the new body, Kuro loses all his previous memory (except for the time being bodyless, then he can remember everything).

“As it turns out, he was no traitor, but instead he couldn’t bear to see his friend that’s fallen in love with such a person as Kuromitsu, which is why he betrayed him.”

He clearly said he’s totally in love with Kuromitsu.

One conclusion could be:
Kuromitsu loves Kuro. She expresses it in a weird way though. She sets up a “game” and let Kuro find her. Therefore, she can pass time (eternity can be pretty boring, hu?) and it somehow follows her ideal of “eternal love”.
As we see the “alternate version” in the ending and the “foreshadow” of the Kuro of the past, we get a broad hint that this is an actual cycle and history repeats itself.
But, there’s room for a lots of interpretations though. Just my 2 cents.

“As it turns out, he was no traitor, but instead he couldn’t bear to see his friend that’s fallen in love with such a person as Kuromitsu, which is why he betrayed him. I’m not sure whether he was actually in love with Kuromitsu, or didn’t see her fit as someone who Kuro should love… it’s there were he obtained a body that wouldn’t die, though over the years, his body did age a bit, as he’s turned into an old man.”

This is a bit wrong. Benkei actually fell in love with Kuromitsu, and he became so infatuated with her that he wished his own master dead. The first time Kuro was beheaded Benkei drank the blood from the beheaded Kuro, and gained a much longer lifespan even if he didn’t become truly immortal.

I also think he said that when he chopped of Kuro’s head the first time, he was under the influence of a curse/spell, but it was made possible because of the conflicting feelings he had towards his master and kuromitsu.