Here's the solution. There's a small code in Project M that makes the stage skip the second part. If you remove that code, the stage won't skip that part anymore.
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Now, the how to:
1- Get this file:
http://www.mediafire.com/download/0y2dmm2cwwuqcpa/SiegeRestore.gct
2- Download this tool of mine:
http://forums.kc-mm.com/Gallery/BrawlView.php?Number=20040
Place both files in your codes folder, where 'RSBE01.gct' is. Open the GCT Fusionizer tool, it will ask you for a file. Select the SiegeRestore.gct file.
Once selected, the tool has two buttons, 'refresh' and 'apply'. Press the 'apply' one, and it will ask you what to do next, as the code has been found in your gct. Select the delete option, the code will be removed from the RSBE01.gct file, and you'll be able to play a 3-stage Castle Siege stage.
It's obvious, but don't play that stage on wi-fi once it's changed back to the original number of transforms.