Hi Jenny,
First, I'm really sorry for what happened to your sister and that you haven't gotten closure on this. I read up on this and did some research and came up with two conclusions that made sense to me and fit the scene. Please let me know if either of these are impossible for one reason or another, or even if it's not your belief that I'm in the right territory here.
I have two scenarios, that to me, fits what we know.
Scenario 1: Drug pickup gone bad. Jody struggled with drugs at an earlier point but was supposedly clean at this point. However, we also know that this might not have been a particularly high point for her. At the very least, she wasn't having a good night. She closed down the bar and wasn't getting along with her boyfriend, and by the looks of the ashtray in the car, she'd possibly been chain-smoking. This happened sometime around 3-4am. The bars were closed. She's sitting in her car making calls. One is to the bartender. My thought was she was going to relapse. She was in bad condition that night and was possibly seeking drugs. Late night phone calls could mean tracking down the right person and maybe she finally did. I also read in one of the articles that she may have stopped at an ATM before she parked. If that was true, my guess is she was looking to buy, making calls to see what she could get. Man shows up, there's a conversation, she has a change of heart. She probably tells herself it was a knee-jerk reaction. Maybe she's sobering up now. Maybe the man at her window scares her. She tells him she's not buying. He accepts this for long enough for her to start to leave and him to start walking away. She's inconvenienced him and she has the money and in the spur of the moment, he decides to kill her. When he follows the car and reaches in, he takes the cash.
Scenario 2: Jody had made several calls that night. It was after 2, so what types of people would she call? One of two I know she made was to a married man she was rumored to have been seeing on the side. This person also doesn't have a very good reputation in town and his wife's car matches the description of the vehicle seen. Jody was told not to come over by her boyfriend. She's lonely and drunk and starts making calls, turning to others for comfort. She calls this man (Don't know if he was an ex, a fling, or if it's even true), he sees the danger in the situation. A girl is calling in the middle of the night. Surely the wife heard the call. If Jody is going down a destructive path, the secret could come out. Maybe she even said something that scared him. He asks to meet. The rest is history. This doesn't answer the question of what was taken from the car though. I'm leaning toward this theory due to the phone calls, the time of night, and it describes a motive.