the problem with the Miranda and actually the Excelsior class at the end of the Dominion war is that it's pretty much the equivalent of running a WWII Frigate that while having electronic updates, is still painfully inadequate for the task against more modern vessels. There was even a mention in the DS9 that the casualty rates were atrocious among these classes because they were antiquated.
Star Trek online Actually kinda got around this with the introduction of the Shi'khar class, which is roughly they same size and design, but updated to more modern. while it is not a warship by any stretch, it at least has the virtue of not being a antiquated rust-bucket probably failing apart at the seems. Never have understood the GM obsession of stating people out in the most crap ship possible....
Anyway: 3 borg cubes? Remember what 1 Cube did at Wolf 359. With what you've just described, that convoy is assimilation bait as those things are 5km square typically. perhaps a Borg sphere? Much smaller but still a credible threat to the flotilla.
Well the ship would be beyond bleeding edge of tech for Starfleet at the time (24th century sensors anyone?), but depending on the amount of hull stress it took, probably not in much of a position to do anything, even after the patch up.
the crew would need to get back home as quickly as possible and probably would need to figure out somewhat to facilitate Slingshot (not advisable in the rustbucket). or some other form of Temporal travel.
perhaps you can use this to make them aware of the Federation Time Fleet or some other time travelling faction that is good or bad depending on what plot twists you feel like throwing there way
A brave little theory, and actually quite coherent for a system of five or seven dimensions -- if only we lived in one.
Academician Prokhor Zakharov, "Now We Are Alone"