Your comments

Buying crystals/items is a one-time payment and the money is deducted once.

There's no information about that anywhere. If you're interested, please set a timer and count how many times the indicator appears. I don't see any other way of finding it out. 

It depends on their rank. Check this for more information.

Micro-Upgrades cost more than simply buying the next modification.

Can you specify the problems? You mentioned you're having a lot of issues. Maybe you can show a screenshot or a video?

If you have M0 and you fully micro-upgrade it, you'll get the characteristics of M1.

If you can buy M1, you'll be given it for free.

If you can't buy M1 because your rank is too high, you'll still get the characteristics of M1 but not the looks of it.

Press 5 on your keyboard.

Press Shift to activate Overdrive.