With practice, it gets easier.
IMHO, the biggest hurdle a newbie have to pass is "letting go".
- Letting go of a bad tree,
- Letting go of a bad/misplaced branch,
- Letting go of a bad/misplaced root,
- etc.
You are lucky that the branches do not have nice ramification at the ends. Imagine a long straight branch with super nice ramified part at the end...and you know you have to remove and rebuild. It will be tough! I encounter those a lot on my collected trees.
Focus on the future...do what is best later not what it will look like now. Do not do it half way either...or you will regret it every time you see it. Do it right the first time. Some things you just have to destroy before you can rebuild. You will be fine.