I have an 88 model samurai that the clutch has burned up on and i am tring to buy a clutch kit.  The local Oreillieys has orderd it for me twice, but it keeps coming in with an issue.  My original clutch is flat at the geared collar on the Fly wheel side.  It was made that way.  I keep getting ones that protrude through the clutch pad by approximately a quarter inch.  That bigger collar does not let the clutch go all the way against the flywheel. Any suggestions? the guy at oreillieys says that all of teh years from like 85 to 2000 use the exact same clutch kit

What part number are they ordering?  Sounds like they might be ordering one for a sidekick, instead of a samurai.  Since samurais weren't imported after 95, he shouldn't be saying they they fit "up to 2000".
A new clutch may not look exactly like your old one.  There is only one way that the fiber plate will fit against the flywheel.  Usually the fiber plate is marked "flywheel side" (or something like that).