Here is what I could find on Fernando Po:
It was the Portuguese who first took Africans as slaves to Europe after 1441. After 1460, they exported between 700 to 800 slaves to Portugal to work on the sugar plantation in Southern Portugal and Spain and the islands of Fernando Po, Sao Tome and Principe
The colonization of the four islands discovered 1471-72 (Sao Thome, Fernando Po, Principe, and Annobon) off the Niger delta would result in yet another experiment. Here the production of sugar would take center stage. Sao Thome possessed soil quite conducive to agricultural production. A greater amount of capital and organization was necessary to establish sugar plantations in Sao Thome with a substantial amount of the capital going towards labor. The next phase in this process resulted in an even greater intensification of the slave trade. In 1471 merchants found a link to interior gold mines on the Gold Coast and were thus forced to provide commodities and prices competitive with the caravan trade. There was a shortage of labor in the region and the Portuguese therefore possessed the bartering tool needed to gain access to this gold market - slaves. Sao Thome became an entrepot for slave trading and substantial amounts of trade occurred between the Portuguese and African dictates with the annual amount of gold being purchased by the Portuguese being measured at about 10, 000 ounces. Later fortresses were built by the Portuguese along the Gulf of Guinea, with Elmina being the most notable among them. This exchange in gold and slaves did not cover the cost of these expeditions and its architect, Prince Henry, died heavily in debt in 1460.
So it seems, like trade was more in Sao Thome but we don't have that, so the closest would be Fernando Po. However, unless there is a 'very' compelling reason, I agree that scenarios should fall in line with the GC. In our GC, many times Portugal fails to colonize Fernando Po (or it does and natives take out its settlement

). So now while that doesn't affect the 1492 or 1520 scenarios, its something of note, and perhaps its why Paradox has that odd Lagos, trading center. So until more research is done, I say put it where you want, because any option we have now is a bit flawed. I also wouldn't remove the Timbuktu CoT until late into the 16th century, as although its power was diminishing it still existed. Besides if Portugal has a CoT in the area, more of the trade will go to Portugal's CoT then the Timbuktu one.
Now in regards to Niani, in West Africa you can never make comparisons to a real map. It just isn't possible given the bizarre warping and the sparsity of provinces. If look in the East, where we have Hausa, in comparison to a real map, the Hausa states should be under PTI, however, the provinces there have the name of Hausa states. If you look in the EEP West Africa thread, I did a whole right up on this. What it comes down to, is that Niani is an important city and although it may be closer to the coast than it was historically, we really just have to accept that fact and move on. I mean we can always do provinces swaps, like I did moving the Bure and Bambuk goldfields to a more historical location (note that Bure should be south of Niani), but is there anywhere better we can put Niani? If such a place can be found great, but I don't think its likely.