I'm at the part of the Main Quest where the quest marker indicates I should talk to Urag gro-Shub in the College of Winterhold.

When I converse with him, there are no topics related to the elder scroll and the quest marker stays on him.

I suspect this may be because I stumbled across Septimus Signus' outpost much earlier in the game (about 20 character levels earlier). So I sorta need to know where I need to go (Aftland) but will my quest marker for the Main Quests ever update to reflect Elder Scroll stuff?

It's really disturbing that the dialogue I'm supposed to have with Urag is not available.

I hope you figured out an answer to this. I'd hate to think you have been stuck there nearly a month.

Anyway, the same thing happened to me. I had completed Septimus' Quest in Blackreach long before the MQ sent me to get the Elder Scroll. Urag gro-Shub wouldn't talk to me about the Elder Scroll either, but you can simply go back to Blackreach, and the elder scroll will be in the machine that inscribed the cube for Septimus (not at the control panel, but in the center of the machine under the lenses).

I did Septimus' Quest before the Main Quest and could simply answer: "Here, I have the Elder Scroll!"
So, I guess, you can simply get the scroll and take it to Parthunax and the Quest will update.

Sady I seem to be in the same position Urag gro-Shub won't talk to me about where to find the Elder Scroll. I read the earlier post about going to Blackreach but can't find it on my map. Spoke to greybeard and he just keeps sending me back to Urag who won't talk about the mission. Help!

Blackreach is a Dwemer ruin found under the Tower of Mzark. So that mean's if you're looking to go there, head to the Tower of Mzark and enter it, then go through it and go underground.

Or better yet, go find Septimus who lives in a cave north, north-west of the mage college. He will give you a quest to go to Blackreach and a cube that needs to be inscribed from the elder scroll. Then you can do both quests at the same time!