Region
Clock Tower map
Three landings
Named parts of the Clock Tower are Foundry Apex, Mechanic's Ascent, and Eastern Summit, and each of those has a Mirror of Life in the fast-travel list. Talos, The Builder, is at the Throne of the Builder with 5,000 health. The real Isaac, The Zealot, is at the Heart of the Clock with 2,500 health.
Sinister Rune is placed at the Eastern Access Shaft. A sage sigil sits at Mechanic's Ascent, beside a shortcut on the left.
Blades and the clock puzzle
Searches ask how to pass the spinning blades and how to get past the clock. No source I used gives a second-by-second pattern. The honest note is that the blade stretch wants Halo of Light and the whip swing, taken on the rhythm of the blades. I will not publish a timing chart I have not timed.
What I ran into
The blade question is the one I most wanted to answer with a count of safe frames. I do not have that count. The page says what ability you need and stops there.
Questions
Where is Talos?
Throne of the Builder in the Clock Tower.
Where is the real Isaac?
Heart of the Clock, at the top. The drawbridge fight in the Main Hall is a phantom and does not drop The Zealot.