Re: 5/3/1 without bench
The reason why the Bench Press gets a bad rep is because it doesn't make you stabilize your midline, you rely on the bench to stabilize yourself; this was mentioned when Rippetoe wrote the Crossfit Total article, and it was decided that the Standing Press was the better alternative, because any exercise done while standing, requires you to stabilize your midline.
Why you want to Bench Press is because it allows you to use way heavier weights then the Standing Press, hence why Rippetoe recommends performing the Bench and Press every other time (one is more "functional"* the other is better for overload).
Dips are phenomenal for assistance for both the Bench and Press, however, they transfer more to the Press then Bench per Bill Starr.
Push Press would be a fine alternative to the Bench, but I'd really only suggest doing that if you don't have a bench; maybe even alternate them every couple cycles or so if you want. I wouldn't have Cleans as a substitute, three Hip driven exercises in a week and only one Shoulder seems a little out of balance, Jim Wendler does suggest to do Cleans before Squats/Deads, something about exciting your CNS.
Hope this was helpful.