The slave cylinder for a 2005-2010 will not fit the front housing of a 2001-2004 TR3650.
I've done a mock-up and believe that you COULD install a 2005+ front housing, but you would also have to use the 2005+ input shaft because the newer housing is deeper and the shafts are longer.
For others thinking about mixing things between these two models, very little will swap. The forks are all different, the tail housings are different and even the main housing.
Even some of the gears themselves are different...
I would think that you can find a hydraulic kit that will slip over the front sleeve and work without creating an awkward, one-off transmission.
1965 5.0 Coupe /MAF/EFI/AOD/B303 Roller Cam
Mustang Manual Transmission Specialist