Just swap the '09 engine in, but use all the sensors from the '00.
Also, transfer the throttle body from the '00, because it's a cable throttle.
Transmission is a different story; don't try it.
2007 Grand Marquis LS: 5.4 swap, 9.9:1 compression ratio, Comp XE268s, NPI pistons, PI heads ported by me, Accufab upper plenum, 75mm DBW throttle body, Factory PI intake with Chinese spacers, CVPI dual exhaust, CVPI torque converter, CVPI air-box and zip tube, J-Mod, 3.55 gears, FMS Trac-Loc differential
17" Dorman CVPI steelies, BFG Comp T/A 255/45 R17s