Completed Discerning the Transmundane quest, Septimus was killed by Daedra god, got Ogma Infinium, but no Elder Scroll in inventory. Can't continue "Elder Knowledge" in main quest. Talked to Greybeards and College of Magic librarian, no options appear regarding Elder Scroll. HELP!!

This may help you retrace your steps:

http://www.uesp.net/wiki/Skyrim:Elder_Knowledge

Thanks, but already tried this. I actually brought the transcibed lexicon to Septimus, but never got the Elder scroll added to my inventory. I think I may be screwed, since I did the Septimus quest long before I got to talk to the old dragon at the Throat of the World.

But in the Transmundane, when you open up the container that houses the Elder Scroll, you get the option to transcribe it with the Lexicon, but it doesn't automatically add it to your Inventory (if I remember correctly...). Meaning that you still have to physically take the Elder Scroll into your possession. Is it possible that you were in a hurry and transcribed the Lexicon but left the actual scroll there?

Not trying to be a [censored], just mentioning a possibility.

Don't read below if you haven't completed Septimus's quests!

Gave the transribed Lexicon to Septimus, and got assigned the Elf Blood gathering part of the quest.
When that was completed, he opens his gateway to Oblivion & dies. Don't know what happened to the Scroll.
Went back to the tower and back to Septimus's outpost, but nothing there. Still having a blast with the
game, but I want to finish the main quest at some point. The game's very particular about most quest items
(can't sell, drop or store many of them), just wish they'd been that way with the Elder Scroll.

Down at the bottom of the page I linked it states quest conflicts under the bugs section. Have you completed the college of winterhold quests? Apparently that can conflict with the elder knowledge quest and cause the librarian not to have the appropriate dialogues until the other quest is done.

The hermaeous mora quest is like a daedric quest and I think is meant to be a quest to lead you getting the scroll. Have you done the Focusing of the Oculary with the light beams? That is the puzzle which contained the elder scroll.

^This. Did you actually take the scroll from the container? Or is it still there?

The Elder Scroll doesn't magically appear in your inventory, you have to walk up to the center of the oculory-thing and pick it up.