You have too much on there. I would split it up. I took the bus from Antigua to Guate city then the bus to Copan. It was very long. I would take the Managua connection out of that equation. Check the bus schedules but think Leon could be dicey right now. By the way when in Copan, also go to Macaw park. I got into Copan mid day then went to the park and went to ruins the next day
Actual time on the bus would be about 12 hours. (Four hours from Copan to San Pedro Sula, three hours to Tegucigalpa, five hours from Tegucigalpa to Leon (or Managua). But connections could be a problem.
You have options to do the Honduras travel - Hedman Alas is the high end bus line, but there are cheaper alternatives.
Tica Bus is the most popular choice for the Honduras-Nicaragua leg. They both have websites with the current schedules to help with planning.
I would recommend going from Copan to the D&D Brewery near the lake in Honduras. From there you can take a shuttle all the way to San Juan del Sur which is close to the border with Costa Rica since the political situation in Leon is tense at the moment.
This is the link for the shuttle tornabe.com/shuttle-from-d-and-d-brewery-to-…