I did change the alpha, in fact I made a new one and replaced the old one, like it tells you in the tutorial. I saved it as the old one. The alpha for that is actually in the image itself as another channel
There is a file in there called this
S3_01661233_00000001_000000000086623A%%+MODL
I tried to open it but only get binary, also I tried to open in in milkshape and got nothing. I'm thinking the shapes could be coded in and not jiust to do ith the alpha. I need someone to think with me, lol, someone who knows a whole lot more than me.
The other item in there was a grey one with no alpha channel that had the circle shape, I removed that out of the equation altogether and deleted it. I thought that might have been controlling the shape but it didn't have any effect at all, the clock still showed up in game like the above image