Just so you know, most people will say do some research, because every question you asked has already been answered.
Yes you will still be able to use the obdII just like a factory 5.3 truck.
Your trans should bolt right up, but I'm not sure if you need a different flex plate than what is used on the v6.
Honestly, I would suggest researching a bit more, finding out what other swaps have been done, look at their parts lists, and go from there. We're helpful, but we won't spoon feed information that can be easily researched. :shake: