I start the clock when I start pouring in the developer and start pouring the developer out 8" before the time is up. It takes me about 15" to get the bleach fully in so there is about a 10" 'error factor' in my changeover. This is normal. Even automated machines have a short delay as the film runs out of one tank into the next. It is accounted for in the process.
As for scanning, here is what I suggest. Scan a frame in as if it were a slide, then we can look at the negative. Scan the same frame as a negative and we see the negative as it should appear as a positive.
This should give us something to work with. I hope that you included a step wedge? This is a great benefit at the early learning stage.