okay, just for convenience, I'll post everything pertinent. I think I see your argument, though I don't know if i necessarily agree yet. I'll think about it here.
okay: Pertinent part of the script:
201 INT. CORUSCANT-SENATE CHAMBER-MAIN ARENA-NIGHTPALPATINE seeks refuge in the vast Senate Chamber. He gets into the Chancellor's Podium and it starts to rise up into the Arena. YODA makes a giant leap into the control pod. The sword fighting is intense in the confined space.
203 INT. CORUSCANT-SENATE CHAMRER-MAIN ARENA-NIGHT
YODA unleashes a ferocious assault on PALPATINE, causing him to almost go over the edge. The Dark Lord drops his lightsaber but recovers with a BLAST OF ENERGY from his hands that surrounds YODA. YODA is deflecting the Sith Lord's lightning bolts.
The energy bolts begin to arc back on the Emperor. It looks as if the Dark Lord is doomed.
YODA: Destroy you I will, just as Master Kenobi, your apprentice will destroy.
YODA jumps to a lower Senate Pod. PALPATINE reaches out with one hand, and a Senate pod is released from its mooring and heads toward the Podium. PALPATINE uses the Force to hurl pod after pod at YODA, who ducks and jumps from one flying pod to another.
YODA leaps away from the pods. He uses the Force to hold one pod suspended in the air. The pod spins and YODA throws it back at PALPATINE, who leaps away at the last moment.
YODA leaps after him, but PALPATINE quickly turns and aims the full force of his energy bolts at the tiny green Jedi, catching him in mid-air and throwing him back hard against the Podium. The force causes YODA to drop his lightsaber. YODA blocks the lightning and throws PALPATINE backwards off the podium. YODA is knocked off the Podium and falls several hundred feet to the base of the Podium. PALPATINE follows in his pod, searching for YODA.
Now, the end of section 201 coincides perfectly with the gap that begins at:
3:26
http://www.youtube.com/watch?v=MFEjcvIRMDo
Alright, now in my opinion, from section 203, this part does not appear:
203 INT. CORUSCANT-SENATE CHAMRER-MAIN ARENA-NIGHTYODA unleashes a ferocious assault on PALPATINE, causing him to almost go over the edge. The Dark Lord drops his lightsaber but recovers with a BLAST OF ENERGY from his hands that surrounds YODA. YODA is deflecting the Sith Lord's lightning bolts.
The energy bolts begin to arc back on the Emperor. It looks as if the Dark Lord is doomed.
YODA: Destroy you I will, just as Master Kenobi, your apprentice will destroy.
And the action picks up again perfectly at:
4:14
http://www.youtube.com/watch?v=MFEjcvIRMDo
Where the script says:
YODA jumps to a lower Senate Pod. PALPATINE reaches out with one hand, and a Senate pod is released from its mooring and heads toward the Podium. PALPATINE uses the Force to hurl pod after pod at YODA, who ducks and jumps from one flying pod to another.
Now, your complaint is that Yoda should have been on the podium, since it says that the "Senate pod heads towards the podium" right? However, since it already says that he has leaped to a lower senate pod, the fact that the mooring headed towards the podium doesn't really change anything, since the next line says they are hurled "at yoda"
The only other difference being that the confrontation with the lightning explosion says Podium in the script, whereas it is on a pod in the movie. However, since the script says that Sidious has "leaped away" already (thanks to Yoda's attack with the pod) it is insinuating that he jumped FROM a pod (as shown to be where he was standing at the break ending at 4:14) onto the Podium. THerefore the only part of the script that directly contradicts the movie is that he leaped onto another pod instead of back onto the podium (which logically he couldn't have been standing on BEFORE "leaping away" when Yoda threw the pod)