I'm not sure what you mean by 'earthquakes' - do you mean there was lots of vibration?
The prop-shaft and the motor shaft should be aligned as precisely as you can manage. Though a universal joint will accept some misalignment, you should aim to get things so precise that there is no need for a joint!
That tube looks rather thin. I use tube which is 10-12mm in OD, with about 3-4 mm thick walls. You are correct that I 'make the shafts larger' by putting little knurled knobs made from aluminium bar on them. if you do not have a lathe, you can buy similar couplings like this:
https://www.cornwallmodelboats.co.uk/acatalog/Robbe-Flexible-Coupling-3.2-4mm-R1445.html#SID=1586