You can use any Sanwa or Seimitsu Joystick, but be sure that yours has the 5-pin connector (IE JLF-TP, not JLF-TM. LS-XX-01, not plain LS-XX) unless if you want to hack the connector. You also need the proper mounting plate (Such as LS-56-01, comes with VF mounting plate, must be swapped for MS mounting plate), but most models come with the proper mounting plate.
You can use any 30mm screw-in or snap-in type buttons for the top panel, like ibeatu said. Snap ins generally work easier, though. Sometimes screwing in the nuts can be a hassle, Sanwa nuts don’t work well with the TE’s Vewlix layout.
While you’re at it, you may want to consider the LizardLick harness for the joystick: http://www.lizardlick.com/JLF-TE-Harness-for-MadCatz-FightSticks_p_615.html They’re more secure than the original harness (held in by glue that won’t exist once you remove it from the original JLF), and can’t be inserted in upside-down, like the original harness. It can cause problems if you switch to a Seimitsu stick, as they have their harness upside-down, and if you forget to flip the connector, only the DOWN direction will work, same deal if you put in upside-down on a Sanwa stick by accident. If you don’t want it, you don’t really need it, but I just find them to be of much higher quality than the original harness, and I think they’re a great piece if you’re swapping joysticks on a TE.
While you’re swapping, you may want to consider different artwork? I mean, if you’re going to be removing the buttons and joystick, anyways, all you have to do is peel the art off and put new art on, and with a plexi cover, you’re good to go.