Luckily, youre not ignoring it, which is why you've posted here in the first place!
What Bruce posted here really boils it down. In your OP you ask if this is normal, and the simple answer is "no".
The second half of your question was if we could suggest a better way to transcribe, but it sounds to me like the problem here is not in how you're transcribing, but in how you're holding your bass. You should have free range of motion in your playing position so you can move easily up, down and across the neck without straining anything. Wrist, elbow, shoulder, anything. If you're muscling the bass at any point, you might need to rethink how you're aproaching your technique.
My apologies if I've misinterpreted what you're really asking here.