People add too many parts to this glitch. This is the simplest way for it.

Clone Pokemon:
1. Go to Battle Fronteir's Battle Tower
2.Depostit OR pick up a pokemon in any box then make sure you place them all in a different plce (not where another pokemon was) or it'll be deleted (i did that once)
3. Save
4.Withdraw (or depending if they were already in the pc) go to the the blue haired lady closest to you (should be on screen)
4.5. Make sure you have at least two pokemon you can use in the challenge
5. Talk to her, select lvl.50 or open lvl
6. She ask you about saving (there will be a 5 second pause)
7. Turn it off right after the pause
8. Turn it on and wala they are in your party and pc

Now there is an easier item clone too. You DO NOT NEED A POKEMON TO BE CLONED for it.

Item Clone Glitch:
1. Go to Battle Fronteir's Battle Tower
2. Select move items
3. Give a random pokemon the item you want to clone
4. Save
5. Take the item from the pokemon (leaving the pokemon in the box)
4. Go to the the blue haired lady closest to you (should be on screen)
4.5. Make sure you have at least two pokemon you can use in the challenge
5. Talk to her, select lvl.50 or open lvl
6. She ask you about saveing (there will be a 5 second pause)
7. Turn it off right after the pause
8. Turn on

There ya go. simplified. You can clone any item that can be held. ( Including master ball in which I have done thing so much I have 567 of them )