Now, I am thinking the original wiring mixed up the loads in the box with the incoming wires and the two neutrals for those breakers have been connected…anyone have thoughts on whats going on?

In order to understand what was going on: put back the original wiring. 100%. Then take your meter and find out why and how it was working.

If the original wiring was working, but still has confused you, then your description for us is bound to be confusing as well, and then we can never know what was reality before (unless we have a very experienced teacher here who has seen it all and knows your confusion in all detail)