[Tsuwabuki]

The first thing to know about Japanese immigration is that every agent has FULL discretion. If they find you even remotely suspicious, technically, they can deny you entry.

On my third tourist visa, at first the agent was very suspicious, and had a right to be, because the law had changed while I was on my first tourist visa. When I came, the law said you could go to the immigration office and change from a tourist visa to a working visa, but it changed in the months I was waiting for my CoE, and they took so long, that my 90 days ran out before it came (and more!). So technically, I was not supposed to be waiting in Japan for my CoE. Once the agent realised that I had a legitimate home to go back to in Korea (as opposed to somewhere far away and expensive to get to, like America), I was no longer considered a risk of overstay, and I got my last visa- and then my CoE came like a week later anyhow.

That being said, I find it highly unlikely that your straight forward easy to understand situation would lead to denial of a landing permit. I've seen crazy immigration stuff, but that would just about take the cake. You have nothing to worry about.