I've been doing GTD since before David called it that, and I can say that my system is never perfect. I'm often changing it because the circumstances of my life change. I remember when I started working for David, he said something like, "Let's try to break your system." It only took a couple of days. But I quickly adjusted my system to my new work. That lasted for about a year, and I had to make adjustments again because my role and type of work changed. That has happened regularly over the years.I do have some perfectionist tendencies ....
Try to be patient with yourself and make it okay that your implementation of GTD will evolve. Hang in there.