Update:
So I pulled out CR3 Lite from my personal console. Having everything wired from my previous setup with Slim Proto V2, I only changed 5V for 3V3. Everything else remained untouched.
Console seems working. It takes forever to boot, but at least it boots. Debug LED on CR3 Lite keeps blinking until boot sequence starts. It does not get stuck like with CR4 XL or Slim Proto V2. I tried tens of starts and each was sooner or later successful.
Now if anyone can advise what is going on here, why console behaves with CR4 and Proto V2 as described in the OP I would really appreciate it. I used all my knowledge, spent dozens of hours with it and now I'm without any more ideas. I RGH'd many consoles but never encountered similar issue.
I don't think I would be satisfied with this result, keeping CR3 Lite inside is a step back. Also the console owner is getting angry because I have this at home several days and he starts thinking that I'm total noob
