Siphon power from the future
I admit that this is a pretty unusual idea, but it simply put goes like this:
You need energy to power the stasis pods and things, therefore you pull a bootstrap paradox. Just make more power when you have time available and send it to the past so that they survive and you learn that you need to send power back so they don't die so that you know you need to send power back.....
You get the point.
Alternatively, (and this could explain near infinite amounts of power in time machines) one could transport power to the time machine using time travel and then just put that power back where it was when you are no longer damaged/have large power sources available. A time machine only needs a large enough battery to be able to cannibalize power at profit. It's not perpetual motion. It's just borrowing power from throughout history to recharge the batteries. Of course, there is a downside to this. One could easily wreck a computer by accident, start electrical fires, or worse kill a person because you siphoned electricity from their body and didn't put it back quite right.
You know... everyday things we see in the world... right?
Now I know what you are going to say.
But the time travel systems broke down
No, their ability to travel through time was destroyed. However, energy movement is probably quite easy. After all, energy = mc^2 which means tremendous amounts of energy are very small in mass once they have been fully processed and so transporting them into the ship could be accomplished via a simple computer component/circuit that the protagonists might not even be aware of. Heck, the additional upside is that since the energy is brought into the ship directly without processing, there is no need for any large-scale power generators. If anything, I would imagine the ship to have massive batteries in the case of system failure, in which case the batteries would serve as a several year backup to prevent complete stranding.
So why doesn't the ship just bootstrap its own power?
Well, that's the thing about a bootstrap paradox. A bootstrap paradox cannot truly create a physical entity. After all, everything ages and decays aside from the very fabric of space-time (which even then is debatable I imagine). So anything in a bootstrap paradox would instantly decay into oblivion. A bootstrap paradox is meant for bringing knowledge in a cycle, or an abstract concept (I believe one story I read once literally involved someone bootstrapping a soul into existence, or maybe bootstrapping it to prevent its nonexistance). Bringing matter in a cycle like that is... impossible.
Why not continually borrow from the future ship and have a generator on board?
That is a perfectly valid option! In fact, this is nothing more than my design, which is intended to be as efficient and small as possible. I'm imagining what I believe would work as a ship that has minimal "extra parts". In essence, the ship merely needs a time travel component and it has power. And the time travel component need not be the same time travel component as the one providing power.
In fact, just to throw one extra thing out there, the computer system on this ship are going to no matter what by far be extremely efficient and fast at processing. The reason for this is that every single thing that does not require interaction by a user can just be bootstrapped to the beginning of the calculation and so... those values were never calculated, just read from memory. Want the first 10 billion prime numbers to be placed in these memory slots in the computer? Fine, it will be sent there instantly.
The only downside that could potentially hurt such a computer is memory management. I'm not saying that the memory would be inefficient, rather what I mean to say is that the computer will have to no matter what spend time sending data to the past and depending on the time travel system, this might take a lot of time. Because of such a fact, a computer system on one of these ships will want to use as little memory as possible and probably doesn't do bootstrapping by default. It is probably a command used in writing the program. Most likely it is something like an if, while, or for statement that says something along the lines of: "bootstrap { code }".
However, I might be quite wrong, actually. Since memory and throughput (the time it takes to process something) generally live in an inverse relationship, the sudden lack of any need to make things efficient for time could lead to data in programs being dramatically reduced at the assembly code and binary levels in a large scale attempt to optimize programming in general in preparation for the new "Temporal Hardware".
And how was this relevant?
Well, I just demonstrated the fact that there is a very obvious use for the time travel technology that is not used for transportation and as a result I have shown that while the characters are truly stranded, they might still have time travel tech on the ship. They just cannot use it to go anywhere due to its size.