Welcome to the world of custom frame world :wink:
I have had many of the same issues as you, just keep working at them and you will conquer them.
I hope that my bike will be fool proof some day, but boy are there many things to work out.
I've found out that you need to draw every detail in a 3-d program. If you do that you won't get surprises like this.
Keep up the good work, it will be worth it at one point