Absolutely. My fastest laps are always the ones where I feel like I am going slowly. You cannot force fast, it has to come naturally and comfortably. When you are pushing the envelope, you naturally tense up which, oddly enough, makes you go slower =)
When I got my last personal best lap, I had absolutely no idea that I had gone as fast as I had. I thought I was a good second+ slower than I actually was...because it was easy, and it flowed naturally.
My last time out at Chuckwalla over Thanksgiving, I dropped four seconds off my previous best (from July) in my first session out. It felt effortless during that session, and I kept wondering why everyone else was going so slowly.
Later that day, my buddy (who I have been 1-2 seconds per lap faster than lately) passed me and quickly put 100yds between us. I fought so hard to keep up and could not. Everything felt hectic and wrong. I also kept thinking something was wrong with my bike, the session just felt like it was the worst I had ridden all day.
I came back into the pits and had dropped another 2 seconds that session.
Sometimes speed comes easily and smoothly, and sometimes I fight tooth and nail for it.
Edit: I like your idea of systematically setting up your markers. I have had a hard time getting markers down because every time I go out to the track, I am dropping time so quickly that as soon as I have a marker set, it becomes useless.
I think for next year I am going to keep a notebook with track maps and markers written down to help me with them.
This past year I would just set corner entry speed by feel, which I found worked pretty well. Most sessions my lap times would be with 1-2 seconds of each other for the whole session (except the out lap).
But speaking to the original intent of this thread, most of the confidence increases for me came through decreasing my lean angles (even at faster speeds) through turns by improving my body position, and trusting that I could feel the tires more.