On a bookshelf across from the door on the opposite wall between tables, look for a book slightly out from the others. ( -127, -32, -140 ) /waypoint -127, -32, -140 (You get access by clicking on a grate in the floor at ( 5, -26, -121 ) /waypoint 5, -26, -121 on the second level down in Stormhold.)
On level 3, next to a cabinet near the Medium of Cron. ( -436, 371, 332 ) /waypoint -435.83, 370.97, 331.70
Sissthra and Rett Runes: You don't have to complete the access quest Summoning the Creator in order to unlock the door leading to the lower levels. When you're in the central chamber and the purple glowing exit is behind you, then the way forward is level 1, the way to the right is level 2.
Voth Rune: You will either have to complete the access quest Entrance into the Obelisk or use the Feerrott zone-in which puts you just inside the Obelisk.
Note: You no longer need to complete any access quests once the zone is greyed out for your character. However, you no longer need to kill the Labyrinth Shadow and the Keeper of Nihility to reach level 3. EDIT: 7/1/18: At 110, I had to complete all unlock quests and kill named bosses to unlock all doors to get to Level 3.
The simplest entrance to the obelisk might be commonlands, take the griffin to Nektulos Station, and then head toward obelisk entrance, kill the shadowed men and you will see a purple glow, click it and you're in or druid or wiz portal to Antonica which is right by an entrance. If you're high level (perhaps on the swashie epic repercussions quest), you may want to pick up several quests, set your aa slider correctly and chrono to level 50 to grind out some xp while you're here, there is even an HQ to kill 100 nightbloods you can pick up in Rivervale (By Hook or by Crook).
In the rearmost right-hand tower (as you enter), a chest on the second floor under the stairs. ( 701, 10, -735 ) /waypoint 701, 10, -735
Instructions for getting good toons into Freeport safely for the Fen rune. There are four guards along the route, all level 45 Heroic, but invis worked on all of them.
From the Commonlands, head to the entrance of the Thieves Way just south of the main Freeport gate. ( -1245, -82, 121 ) /waypoint -1245, -82, 121
Enter the Thieves Way. The entrance to Freeport North is across the room. Find a click-able grate in the wall. All four portals to the different districts of Freeport are in this room, so make sure you enter North Freeport. ( -123, 1, 50 ) /waypoint -123, 1, 50
Enter North Freeport. Follow the wall away from the sewer entrance until you see a ramp going upward to your right. Take the ramp. A guard stands at the bottom of the ramp.
The Academy of Arcane Science is at the top of ramp. There are two guards at the door of the academy, but no other potential attackers.
Enter the academy, turn left, and take the left elevator to the upper balcony.
There is one last skeleton guard standing watch up here, but if you keep to the ledge, you can get to the book without aggro. If using invis, it will break when you click on the book.
Get your rune from the book (green book standing on edge on the table) and port out.