If its a consolation flying VFR didn't really click completely with me until after 100 hours as a flight instructor so about 320 hours. Before that I thought I knew what I was doing passed all the exams etc but really was going through the motions with what I had been taught. After it clicked I knew what I was doing and the actual control inputs were automatic. I just needed to think I want to be over there in xxx config at yy speed and it would happen while I was spouting the theory and demonstrating while knowing what all the other traffic on frequency was doing. I suppose a bit like when you realise you haven't thought about changing gear or what you did with the clutch in a car on a hill start.
IFR it was after the first winter so was about 500 hours. Before that I didn't have a clue what was going on around me looking back. I only knew what was going to happen in 5 mins time.
These days it automatic for me to think flights in advance and 6 day blocks. The individual flights are just revolutions of the same procedures and its more maint, flight duty times, operation planning issues etc etc The flying is the fun part when nobody can phone me up. But that's the life of a commercial Captain.
Its completely normal so don't worry about it.