The useful data is all in the Entity array. This array is made up of two kinds of objects, tripUpdates and vehicles. These objects come in pairs, which are probably in sequence in the array. Each has an id property, which will not refer always to the same train between API responses.
Each vehicle or tripUpdate item will have a trip property that will be the same between the pairs. This has a tripId property which can be used to identify the train in future API responses, and shows the train's line designation, and direction (all trains in the system are classified as either N or S). It also has a frustratingly HH:MM:SS formatted timestamp for when the train started (or will start) its journey.
"trip": {
"tripId": "081600_A..N",
"startTime": "13:36:00",
"startDate": "20200902",
"routeId": "A"
}
A vehicle object has information about the current status of the train. The trip property will stay consistent throughout the train's journey in future API responses. tripUpdate objects have a matching trip property. The currentStopSequence counts the number of stops the train has made on the current journey. This may refer to a different stop depending on things like if the train is local or express. stopId refers to the last station the train stopped at. The MTA mantains a list of all the stations in the system where this stopId is called the GTFS StopId.
"vehicle": {
"trip": {
"tripId": "081600_A..N",
"startTime": "13:36:00",
"startDate": "20200902",
"routeId": "A"
},
"currentStopSequence": 35,
"stopId": "A05"
}
A tripUpdate object has information about where the train will be in the future. The stopTimeUpdate property is an array of future stops with arrival/departure timestamps (from what I've seen these timestamps are always the same), and a stopId. The example below shows a train near the end of its journey with only 2 stops to go.
"tripUpdate": {
"trip": {
"tripId": "081600_A..N",
"startTime": "13:36:00",
"startDate": "20200902",
"routeId": "A"
},
"stopTimeUpdate": [
{
"arrival": { "time": "1599074067" },
"departure": { "time": "1599074067" },
"stopId": "A03N"
},
{
"arrival": { "time": "1599074262" },
"departure": { "time": "1599074262" },
"stopId": "A02N"
}
]
}