Any update? I have the same issue on my 2003 Yukon with LQ4 swap. Worked fine before the swap, but it took me about 6 months to get it buttoned up and ever since then it has the extended crank after being ran. It sometimes has the extended crank when cold, but always when hot. I just turn the key and let it crank 4-5 times, key off, then it fires right up like nothing happened and runs great. I checked the fuel pressure on mine and it does leak down below 45 within an hour. I have all 5.3 stock components minus the block and heads. I sure don't want to throw money at it replacing all the things you did.
I guess the moral of the story is to not swap in a 6.0.
I guess the moral of the story is to not swap in a 6.0.