http://www.youtube.com/watch?v=nSNHk2GcISU . Also, the "1/4 turn mark" is relative to where a skater leaves the ice. She doesn't even take off perpendicular to the side board, she takes off a little bit before that point, which means the "1/4 turn mark" should actually be seen as slightly further back. Jumps also have a natural ride-out of 1/2 rotation on the landing. Look at where her skate is exiting the jump. Even the sound of the landing is correct to my ear!
Her first 3Lo was iffy but I don't believe that one was even more than 1/4 turn either, when you look at where she actually leaves the ice. Callers are supposed to give the benefit of the doubt. Of course, if they don't properly measure where a jump actually begins, then they are going to be off. They basically just call jumps as < when they see a skid on the landing, which is not correct. Jumps can be within the 1/4 and still have some skid on the landing (of course they can be underrotated and still appear smooth on the landing as well).
If Murakami's jumps had been judged as 3Lo+2T with 0 GOE and 3Lo with +1 GOE, and Kostner's 3T in the SP had been called <, the standings actually wouldn't have changed solely based on the tech mark. You are correct about that. Kostner would have still won the Silver over Mao by a little over .1 of a point and Murakami still would have been behind Mao. However, these bad tech calls are just one part of the problem. I feel Kostner and Asada were both overly gifted in the PCS as well. If you lower those scores by just a few points in total, between both the SP and LP, then Murakami is the Silver medalist.