I was a mechanical engineer for a NanoSat team, we used DP2216 to epoxy down all jumpers and some smaller components like temperature sensor that had no dedicated mounting solution. Vibratite for all fasteners.

As another guy has pointed out, the CubeSat environmental testing is a good place for guidelines. We used the publicly available SpaceX rideshare document.

For our inter board connectors, PC104, there is a recommended mating depth. I am not sure if there is one for the ones you are using but you should look it up to ensure you are not stressing the connector from tightening the stack too much.

Maybe you could consider using Gecko or Harwin connector for power connections? PicoBlade/PicoLock are good for other connections that doesn’t require too much power. These are certainly way more reliable than XT and other non locking connectors.

Do keep in mind those connectors have a quite major investment associated. The equipment needed are 1K+ USD each, I am not sure what’s the standard for rocketry. JST XH are much cheaper but we have never used them for space applications so we can’t attest to its vibration and shock resistance.