Won't you have to pull the head off to get the pistons out to replace the rod bushings and pins?
No. Your crank will maintain the same position. It will take about 8 hrs to do that size engine.
About inspecting pistons, that's a personnal call. If your not loosing compression and not using oil I wouldn't bother. What does the lab say about your oil samples?? If your oil sample says theres a trace or more of Antifreeze then maybe. When you drop the pan and pull number one you can tell whats happening. I used to do mine that way before R/R the engine. I always did my own way back before the engines would go a million miles w/o an issue. I would do the bottom end in old Cat engines at about 400K. When I had 12 Petes with Cats I had a spare engine build on the shop floor ready to go. But times have changed and it's not cost effective anymore.
Oh yes you need to line the timing mark to top dead center than all the rods will be easy to get to.
In adding. I guess you have not been doing oil samples or this would have been picked up with metal samples. Always do oil samples on every oil change. One simple thing can be left undone and it can cost you 20+K to fix it.