Did the SPD ever get a search warrant to access that phone or the phone records?
Not before they declared the investigation complete. I think what they asked for was a subpoena, not a warrant.
If the order was granted eventually, I guess it would be transferable to SAO/FDLE, as the authorities currently investigating the case, rather than them having to start the process over from scratch.
Early in his interview of Dee Dee, de la Rionda said something about having all the phone records.
Who has the phone currently?
I don't know, but I know of no reason to think it isn't with the other evidence. Evidence in a criminal case typically isn't released until the case is resolved.
I'm guessing it's all still in the SPD evidence lock-up. SAO/FDLE had to go to Sanford to interview witnesses, so they could look at evidence at the same time. Every time evidence is moved it complicates the chain of custody, and there's a chance of something getting lost. I wouldn't expect evidence to be moved until it's needed in court.