You would've struggled to get the shims in if the pads are that tight anyway. There shouldn't be any high spots or irregularities with the rotors so there is an issue. It looks like you have been thorough with your prep and assembly, it might be down to how thick the pads are out of the box. If you are still getting a spongy pedal you either still have air in the system or the master is bypassing. Brakes can be problematic - you can do them 10 times without issues and then something will throw a spanner in the works.