You've got multiple issues, only one of which is IRO's problem.
You shouldn't have to pay shipping to or fro for warranty issues.
Why did it take you 2 years to ID and try to solve this problem? It should have taken 20 minutes of head scratching during the initial build. Which leads me to the next point...
You wouldn't have this problem if you went to a local bike shop. You'd get over the counter warranty service. That's what they do.