The '00-'02 V6es had an optional 5-speed manual gearbox, but that's it. And no, that Getrag unit isn't rated to handle the output of the 3.9L V8.
To put a manual transmission in an LS, you should be able to use the gearbox from the '05 and newer Mustangs (the floorpan was one of the few things the Mustang inherited from the LS), but dang near everything else will be custom (read "$$$$$"). You'll need a custom bellhousing, possibly a custom flywheel, a custom driveshaft (no u-joint yoke on the LS), and custom brackets for the custom clutch and brake pedals. You might be able to adapt the factory V6 pedal assembly, if you could find the parts (they made fewer than 1200 LSes with manual transmissions).
And, oh yeah, you'll need an XCal and a knowledgeable SCT tuner (like ILLS or Torrie) who can go through the PCM code to find and eradicate all of the errors that'll be thrown when the PCM looks for signals from the non-existent tranny.
It can be done, but it's certainly not a trivial (or inexpensive) project.