A pan drop only got about 1/3 of the old fluid out, that's why it's dark again. Do a complete exchange with a machine. Should take about 14 quarts, pan only holds 5 quarts. Most of the rest of it is in the torque converter.

Motorcraft plugs, no antiseize, 28 ft/lb torque. Boot/spring kits are not brand-critical, just use a bit of dielectric grease in the boots, taking care not to get grease on the springs.