[khorboth]

My first thought is aligning the FTL drive with the STL drive and/or the artificial gravity. A small misalignment will mean a sudden apparent gravity shift and some crushing damage. A major misalignment will mean a sudden apparent gravity shift and massive crushing damage. Going back into FTL before alignment is perfect could be fatal.

A problem could also be had with the databases. We need to rebuild them before we can safely travel because gravitational waves (a real thing) can throw us light-years off-course and we may not have enough fuel to get home. To rebuild them, we need... Computer Programming. Astronomy. Electronics Repair. Astrogation. A working telescope Etc.

What if the FTL drive won't come fully off-line? then somebody has to crawl inside the working mechanism and find the sticking point. Roll DX for progress (failure may result in crushing damage). HT to resist heat (failrure my result in fatigue damage). And a repair skill to find/repair the problem. Radiation damage may also apply, but IDHMBWM. Every (random) minutes the ship lurches in/out of warp throwing everybody around and damaging the ship further until it's shut down properly.

The Fredrickson Actuator (not a real thing) came loose from its housing and careened through several other parts. They can be scrounged from other systems, but.... do you want to do without weapons? shields? Life support? Navigation? Sensors? Choose wisely.

Just some ideas off the top of my head.