The graph shows the flyby geometry in the geocentric mean equator and equinox of J2000 reference frame.
According to the NAIF's files, the change in the velocity vector was 6005 m/s.

The altitude (shown in km as "h= ..." when you hover the mouse over a point) is calculated above an ellipsoid with an equatorial radius of 6378.1366 km and a polar radius of 6356.7519 km.
The popup label also shows, in km/s, the geocentric speed (Vgeo) and the heliocentric speed (Vsun) of the spacecraft.

The blue line represents the Earth's heliocentric velocity vector, while the yellow line points toward the Sun (both lines lie almost exactly in the J2000 ecliptic plane).

The values obtained for the perigee are:

	time: 2005-03-04 22:09:14.120 UTC
	radius vector: 8331.798 km
	geocentric speed: 10.5170 km/s
	location: 20.3031, -113.2579
	altitude: 1956.221 km

Here's the path across the Earth's surface.

The values obtained for the lowest altitude above the WGS-84 ellipsoid are:

	time: 2005-03-04 22:09:15.263 UTC
	radius vector: 8331.803 km
	geocentric speed: 10.5170 km/s
	location: 20.2625, -113.3395
	altitude: 1956.216 km

Here's the distance between the spacecraft and the Earth (blue plot) and the spacecraft speed wrt the Sun (orange plot).
The green vertical lines represent the Earth sphere of influence (the distance from the Earth where the gravitational acceleration of the Earth and of the Sun are the same).

The spacecraft heliocentric speed increased from about 30 km/s before the SOI to about 34.2 km/s after the SOI (the Earth's heliocentric speed near the flyby epoch was 30.034 km/s).

The change in the velocity vector was 5210 m/s.

The values obtained for the perigee are:

	time: 2007-11-13 20:57:22.962 UTC
	radius vector: 11672.994 km
	geocentric speed: 12.4877 km/s
	location: -64.6373, -65.9881
	altitude: 5312.301 km

The values obtained for the lowest altitude above the WGS-84 ellipsoid are:

	time: 2007-11-13 20:57:23.241 UTC
	radius vector: 11672.994 km
	geocentric speed: 12.4877 km/s
	location: -64.6346, -66.0287
	altitude: 5312.301 km

The spacecraft heliocentric speed increased from about 32.3 km/s before the SOI to about 35.3 km/s after the SOI (the Earth's heliocentric speed near the flyby epoch was 30.107 km/s).

The change in the velocity vector was 6252 m/s.

The values obtained for the perigee are:

	time: 2009-11-13 07:45:39.987 UTC
	radius vector: 8857.659 km
	geocentric speed: 13.3405 km/s
	location: -8.1467, 109.0076
	altitude: 2479.949 km

The values obtained for the lowest altitude above the WGS-84 ellipsoid are:

	time: 2009-11-13 07:45:40.222 UTC
	radius vector: 8857.660 km
	geocentric speed: 13.3405 km/s
	location: -8.1387, 108.9877
	altitude: 2479.949 km

The spacecraft heliocentric speed increased from about 35.2 km/s before the SOI to about 38.9 km/s after the SOI (the Earth's heliocentric speed near the flyby epoch was 30.105 km/s).