ok, i finally got around to finishing the main quest thanks to the most recent patch, which fixed my game, again... bethesda is doin a good job with these, as far as i can see from my end.

anyway, i never bothered with the civil war, so i had to do the peace negotiations... apparently, the stormcloaks rule markarth now.

great... i never completed the forsworn conspiracy!

will the changing of the jarl and everything screw me over with that quest, as well as any other quests markarth has that i may not have done yet?

i havent touched the civil war questline yet, just to reiterate.

oh, and i suppose the same question goes for riften... because i traded markarth for riften, and mostly sided with the imperials, so i essentially pissed off ulfric i guess... will riften becoming the empire's end up effecting any quests there?

also, just wondering... did anyone else get excited at the cutscene of our character climbing onto odahviing's neck and flying off into the sky for the final part of the main quest?

it was a short scene, yeah... but we technically got to ride a dragon... that was awesome.

Ok well basically the only problem you can potentially come across, unsure if its patched or not.

Is the Cidna Mine quest in Markarth.
If this does bug out for you heres how to fix it.

1. Finish the quest, make sure every last bit of it is done.
2. Leave and never return.
3. Do the Civil war, you will have to side with the imperials
4. Once the war is over, Markarth should love you again

In terms of changing the Civil War quest chain by the MQ I found that when I did the Civil war following the MQ that I only attack camps, assisted in the battle for Whiterun and then attacked the opposing forces city.