You should keep your current bellhousing. You could use the newer external, but the slave will be on the other side, so you'd have to deal with a new clutch line.
You cannot swap on the 01 flywheel. As far as the clutch is concerned, they're all the same, but the flywheel needs to stay with the generation of the control system.
I do have a concern though, 00-01 2.5s are almost unheard of. This AX-5 is from a 2.5, and not an AX-15 from a 4.0, correct?