It would not end well. Northern Nigeria would have the highest population of any landlocked country in the world (at least until Ethiopia became landlocked, assuming it even does TTL). They will ABSOLUTELY want the rights to navigate the Niger River and will probably do anything they can to get it. It will still have many ethnoreligious tensions since there is a large Christian minority in the south of the country as well as many ethnicities who only recently converted to Islam.
Southern Nigeria isn't much better. It still has the issues of distribution of oil money and will be split between a Yoruba bloc and an Igbo bloc with the other ethnic groups in-between. I could see Biafra still attempting to break away in this situation, and TTL likely supported by Nothern Nigeria either covertly (arming Biafra and sending fighters there) or overtly (open war against Southern Nigeria). Based on this, I think Biafra will win and possibly even manage to carve out the Republic of Benin (not to be confused with modern Benin, this Benin would be mostly an Edo state centered on Benin City) as a buffer state. Both of these would be heavily influenced by Northern Nigeria and Northern Nigeria would get their rights to the Niger River thanks to this. They would be heavily involved in keeping the river dredged to at least Lokoja (probable site of their main "seaport") more than the OTL Nigerian government is.
Politically Northern Nigeria will probably become an Islamic republic at some point with local interpretation of Sharia law enforced in every state.