It is perfectly normal if your battery health (maximum capacity) is more or less than 100%, even when brand new, or if it fluctuates up or down over time. For further details, read the CHECKING STATUS AND HEALTH section of the following link.
The link below should answer most, if not all, of your battery/charging questions. If you haven't already done so, I highly recommend you take the time to read it.
No, that had nothing to do with it. Some batteries show over 100% when new, some less. It's only an estimate, after all, and will fluctuate up and down over time.
You don't. While it will fluctuate over time, the general direction is down, as all batteries deplete and die over time. Just use your Mac and don't obsess on the battery readings.
Run on battery whenever you need to and plug it in whenever you can. You can plug or unplug any time you need to, regardless of the charged percentage, and you never need to completely drain your battery. Just make sure you don't run on AC power exclusively, as your battery needs to be used regularly to stay healthy.
It is like that on purpose to prevent overcharging. Unless you run it down below 90% or so, it will hover around the 90s. Unplug it and use it today until it gets down well below 90, then plug it back in. I bet you will see it get closer to 100 then.