The main reporter for the NY Times story wrote it from Sepang Malaysia, he was assisted by two reporters in Washington.
The climb to 45,000 ft, the descent to 23,000 ft, are based on Malaysian military radar. The 40,000 foot descent in one minute is based on engine data, and is discounted as unreliable by 'investigators'. (The source for the 40,000 foot descent reference was a Washington official.) The two initial course changes, and flight then stabilizing at a cruise altitude of 29,500 feet are based on Malaysian military radar.
The NY Times article does not reference the VAMPI, GIVAL, IGREX waypoints.
The VAMPI waypoint looks to be near the island of Pulan Perak, where earlier reports said Malaysian military radar lost track of it.
GIVAL is about 54 NM from VAMPI.