It does look odd, but it could just be the photo. The clip is definitely wrong but that shouldn't cause the issue you're having.
So next thing to try. Again with your assistant, get them to push the pedal down and check that the pushrod extends out of the slave cylinder by 1/2".
At this stage, until you have it all working, I would unwind the big throw out nuts so they are well clear of the wok.
Thx Grame will try that later when I get home from work and push rod extends well beyond 1/2 inches from memory (will send a pic) - I use a 4 foot long level as my assistant - wedge against inner door.