Did El Niño extend all the way to the West Coast of Africa? Did the meridional overturning circulation exist back then? Was there another overturning circulation that existed?
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Concerning the thermohaline circulation: the defining part of it, I think, is the formation of bottom water in the polar regions.
The formation of Antarctic Bottom Water (AABW) in the Southern Ocean is strongly linked to the presence of the Antarctic Circumpolar current (ACC). The ACC was possible only after the opening of the Tasmanian Gateway and the Drake Passage (between Antarctica & South America) which both happened in the Late Eocene / earliest Oligocene. The ACC is thought to have been the deep, strong current it is today since the Late Oligocene at the very latest (Lyle et al. 2008), so the AABW is also thought to have existed since the Oligocene.
However as far as the North Atlantic Deep Water (NADW) formation is concerned: it is linked indeed in part to the Gulf Stream and the Northern Hemisphere glaciation. While the latter only occurred ca. 3.6Ma (e. g. Muddelsee & Raymo 2005), the Gulf Stream is a direct consequence of the closure of the isthmus of Panama: the shallowing (and therefore closure to deep current) of the Panama Seaway is thought to have happenned at ca. 4.6Ma (Haug & Tiedemann 1998) with a complete closure at 2.6Ma (Lunt et al. 2008).
So it is rather safe to say that the thermohaline circulation as we know it today settled probably around 3.6Ma (therefore mid-Pliocene).
Back in the Eocene (55 to 33Ma), the formation of bottom water is thought to have occurred in middle to low latitude (e. g. Kennett & Stott 1990) leading to a very completely different kind of global circulation.
The impact on the ENSO (if it existed at the time) is, as far as I know, unknown but since South America was still here to limit it eastward I don't think it ever reached Africa.