I'm sorry that the city fell short of OP's expectations but I have a feeling that may have more to do with those expectations than the city itself.
You can't possibly get a feel for the city in two days, I'm sorry but that's simple. I've spent a similar amount of time in Washington and been to the main tourist sites, I wouldn't dare say that gave me a feel for life or what passes for local culture there. The city is rather run down in parts, that's true but then I could say that of many places, not just in Brazil but around the world.
The African influence is all around but don't come with the expectation that you are being transported to Lagos, Conakri or some Disneyworld representation where the natives sing and dance and spend their days perform authentic rituals for the delectation of tourists. It's a city of three million people.
Afro-Brazilian influence is most readily accessible in the food, in music, dance and art. It is all around you, it's just not a folkloric presentation.
There are any number of restaurants that will provide you with the first, although if you want to get a ready introduction to the range of Bahian cuisine, the SENAC cookery school in the Pelourinho with its buffet is a good start. Then of course you have famous institutions like Sorriso da Dadá, Dinha's, Iemanjá, Aconchego da Zuzu, Boca de Galinha etc etc. The list is endless. That's not counting all the street stalls, serving things like acarajé. The dendé oil many dishes are cooked in? That's African jusr as manioc, which is Brazilian has become a staple in Africa ( historically becuase it was a cheap food that could be grown near the slave barraccons in Africa to sustain slaves on their trans-Atlantic voyage).
Music, well attending the Pelourinho on Tuesday nights is one way but there are plenty of artists performing on other nights in other places, there are greatplaces to hear live music in other post like Garcia, Liberdade etc. Olodum has a school in the Pelourinho and there's always Liberdade. If you want to see an inspirational project that features music then Carlinhos Brown's Pracatum school in Candeal is open to visitors. Easy to get to by cab from Shopping Iguatemi. Candeal itself is well worth visiting.
Salvador is famous for its capoeira schools. Did you venture to any to take a look? I don't mean the clowns behind the Mercado Modelo, who try and blackmail tourists who take photographs. A number are open to visitors.
The tourist shops in the Pelourinho are not the best way to find local art but that's true of any city. I would't expect to find a Caravaggio at a gift shop in Rome. Bahia is best known for art naif, even if its most well known artists haven't necessarily painted in this style. You need to explore the private galleries. Too many for me to list here I'm afraid.
For what it is worth there is an excellent Afro-Brazilian cultural centre in the form of the Museu Afro Brasileiro if you want to explore the history and influence of African culture. Had you visited the modern art museum in the de União or eaten in it's restaurant you would have been in teh midst of that culture. The senzala, the slave quarters are still there. Excellent food btw.
A little knowledge of the city doesn't hurt. Knowing which neighbourhoodswere former quilombos, like Liberdade will give you a picture of African history Knowing what the balangadas on the Baianas symbolise will give you a sense of the roots of Brazil.
As for popular festivals with Afro-Brazilian culture, I'm sorry but you came at the wrong time of year. December to February is crowded with festivals culminating in the Festa de Iemanjá. That really is a unique and unmissable event if you are in town.
The OP seems to be suffering under a not uncommon misapprehension about candomblé. Presumbaly the 'main candomblé church' referred to was Bonfim, unless of course they mean NS Rosario dos Pretos. Candomblé is, in part, a syncretic religion where Catholicism and its rituals and saints are identified with their African counterparts. Hence the Virgin Mary doubles as Iemanjá etc. I won't go into the historical reasons but suffice to say until relatively recent times candomblé was either actively suppressed or looked down upon.Iif you vist Bonfim, don't expect it to be anything other than a Catholic church, which is what it is. Where you will see the interaction between the two is at festivals. That said there's plenty of African influence on display in the Catholic churches. NS Rosario do Pretos in the Pelourinho is the first church to have been built by freed slaves in Brazil and probably anywhere in the Americas. I was married there,as it happens. Had you come to my wedding you could have had your fill of the Afro-Brazilian influence you sought. If you had visited Salvador's most famous church, Igreja de São Francisco you would have seen the carvings of rather naughty angels and cherubs with African features.
Beyond that if you are looking to experience a candomblé ceremeony you will need to visit a terreiro and most of these are located in parts of town you won't easily find, some of those areas are none to safe. Some are quite welcoming of visitors and can be viisted if you arrange something with a guide. For serious students of the religion, UFBA, the local federal university, has a listing of all the extant terreiros in Salvador.
African influence is all around you, you just need to know what you are looking at. Fortunately nearly all of this information is out there in various guides, on line sites about the city etc, etc. The OP is to be commeded for at least looking for it. Many years ago my wife was showing two Portuguese tourista around town and one of them asked her "why are there so many black people here?" My wife gave a very neat response "because you brought us here".
Happy travels and do come back some day.