You lost me after you suggested that Madara used Orochimaru to transplant the Rinnegan into Nagato. Why would Orochimaru ever give up a good pair of Rinnegan eyes once he got his hands on them? The eyes that would allow him to discover all jutsu his dream mind you. Not only that how did Madara still operate once he gave his own eyes to Nagato did he waltz around blind? This was before the Uchiha massacre there is no library of sharingan eyes to fall back on, Obito hadn't been crushed by a boulder yet, and his old eyes became blinded long ago when he used MS too much which was the entire reason he had to replace them in the first place so switching back wouldn't work he would simply be left in the dark unable to do the things that Tobi was said to do like control the Mizukage. Sorry but you didn't fill any of the still blatant plot holes.