Dug through the game files and found the appropriate on_action trigger to re-add in the random damage event. It should now only fire on arrival into a system.

Note: It will damage all ships in a fleet, whether that's just the science ship, or all 100 corvettes you have. The damage should be minimal, but will add up quickly, and there's the chance that all your ships could be heavily damaged, or even destroyed!

As always, let me know if you run into any issues, or if you have any balancing suggestions!

There was an issue with an event that damaged any ship that used the experimental drive.

It was intended to damage the ship on arrival to any star system, and relied on some older triggers/modifiers that are no longer supported (likely holdovers from pre-2.0 stellaris). Instead of firing on arrival, it was firing monthly.

Unfortunately I am unable to find a way to update this part of the event to a working version, though will keep playing with it. It was a minor flavor addition, and this mod will still be 100% functional. Other code in this event remains as it is still functional, and is not flavor.

Thanks to everyone who's trying this out and keeping me updated on issues you run into!

Version 2.7.2.1
Changes that have been made, bringing the mod up-to-date with 2.7.2

Update:
Updated component restrictions to allow the attachment of the new hyperdrives to the juggernaught class of ships
Updated Physics tech file (It's necessary to overwrite the whole tech-tree to allow for the experimental drive tech to function properly) to be compatible with new ascension perk, and Federations DLC

Bug-fix:
Between Andon's bug-fix, and a tweak to the experimental drive that I've made there shouldn't be any issues with ships not arriving at their destination. Please let me know if the issue persists. To this point, after making my final tweaks here, I've been unable to re-create that particular issue.

QOL Improvement:
Added necessary files to add the ability to customize civilian ships to allow the player to attach the new FTL drives without the need for a second mod.

-Note: This new functionality does not apply to the private colony ships. Since they are private, I feel you shouldn't be able to customize them. It isn't your ship after all, but more like a charter. This unfortunately means they must be built in the system you want to use them for now. If I can figure out how to get the auto ship builder to use them I'll change it that way, if not then they may be adjusted to be customizable later.
-Note: This QOL improvement should be compatible with shipset mods that utilize the base-game ship_class classification system, and explicitly define civilian ships. A mod that uses different ship_class definitions may not allow the experimental drive to be attached. A mod that doesn't explicitly define their civilian ships, and instead use a pre-built version of a civ. ship (not sure how to explain this better) may not allow you to customize those ships. Shouldn't run into it too much, but if there's a popular mod that does do this, I may be able to patch it if the interest is present.