As Jay said, the killer was Adnan. The two calls made at 2:36pm and 3:15pm were both from Adnan. The first was made at school. The second was placed in/around Best Buy, during which Adnan told Jay to pick him up at the front entrance (only entrance?) of Best Buy.
There were reports where witnesses said that they saw or talked to Hae up until this time of the first call to Jay at 2:36pm. The 2:36pm incoming call was probably Adnan calling Jay from school to say, as he mentioned in Intercept and I'm paraphrasing here, "I'm gonna do it." Jay was at Jenn's house. Maybe he said, "see you at Best Buy or come get me at Best Buy."
Adnan, did in fact get a ride from Hae. They drove to Best Buy where they could have a private moment to talk, as per Adnan's suggestion. He killed Hae. There WAS enough time between 2:36pm and 3:15pm to drive from school, commit the crime, look for a payphone and place a second call to Jay at 3:15pm. During this second call, which was actually longer than the first, Adnan told Jay that he would be at the front entrance of Best Buy. Or maybe he had to make the call because he couldn't find Jay at Best Buy.
There was also a significant amount of time between 3:15pm and the next call at 3:21pm. It probably took some time before Jay found Adnan after that call. The two of them had a conversation. Jay was in shock. Jay called Jenn. Were they looking for pot at this time?
I think Jay was confusing a lot of the details of that day. His timing of events was off. He probably mixed up two or three events that happened during different times of the day and thought they all happened right around the same time, or vice versa.
Also, he mentioned in the Intercept interview that he was "stonewalling" the cops. He wanted to protect some people. Let's not forget that he was dealing drugs and as he mentioned, he was scared for his and his grandmother's life.
These reasons could account for the changes in his story, plus the police trying to work his story into THEIR timeline. It's understandable that Jay would have different versions of what happened. I do the same when I try to piece together details of a traumatic event.
It's interesting how I came away thinking that Adnan was innocent after listening to Serial. Now, after further plodding at some evidence, I find myself doubting that Adnan did not kill Hae. If the police were not too hung up on the cell phone timeline, they might have been able to come closer to the true timeline of events (placing the burial at 7-8pm because the cell phone pinged Leakin Park at this time, instead of thinking that it might have happened later that night).
Finally, the fact that Jay was scared of the drug dealers that he worked for compromised his original testimonies. Only three (or four) people know the truth and one of them can't really speak for herself: Hae, Jay, Adnan (and the killer).