(Yes, yes, they built a new intermix chamber, which is the point, if every time they increased the potency of the corpse fuel, they had to redesign and rebuild the engine, it must have got to the point that its easier to ignore further refinements on the fuel, so they don't have to spend another year rebuilding the engine.)
Or the modifications would have entailed not changing the engine at all... just the intermix chamber would have been modified on the go. Base design would have been more or less sound, so it would be like ADDING stuff to pre-existing design to make it more efficient.
Making a new intermix chamber every single time would be a daunting task for the Equinox due to replicators not being available... although, they'd probably still have the ability to emulate replication with other tools manually (by converting existing hw into base elements and recombining them into new ones)... in which case, minor adjustments with each fuel refinement would have occurred.
A bigger question would be: 'how did the Equniox withstand travel at such high Warp velocities' when it wasn't designed for those speeds? At maximum, the Nova class was capable of Warp 6 (per Janeway's description).
Sure, a refit with faster engines (more capable Warp coils) and stronger structural integrity would have done the trick to make it capable of say Warp 9.9 at some point in the future, but to produce that kind of SIF effect, you'd also need stronger power generation.. and in its weakened state, I don't see that happening.
The best way I could describe it is that the corpse produced 'super-charged anti-matter' which resulted in much higher power output in the Warp core... but again, if the engines weren't designed to operate at those levels... shouldn't the ship basically tear itself apart?
Voyager was able to last 9.5 seconds in that Kes' telekinetic push which pushed them 9.5 thousand lightyears closer to the AQ... but that was a more extreme burst (and the ship was at the brink of coming apart).
And Warp 9.75 (not 9.975)for Voyager was sustainable for about 12-24 hrs.
Ransom said the Equinox pushed through 10 000 Ly's in less than a week... which would imply a speed of Warp 9.95 (or about 1882.56 Ly's per day).
If the Equinox was designed to max out at Warp 6, could the SIF and engines be supercharged enough to withstand Warp 9.95 for 5 and a half to 6 days?
A standard handshake between the ships computers, should have seen the transfers of each others logs to the other's possession. Ransom may have lied about what happened in Ankari space, but from a navigational point of view, lying about the existence of, or the names of planets is a good way to get caught telling a lie.
Remember Ransom said making a deal with the Borg sounded like Treason? So he had read her logs, and Janeway must have read his.
Smart people hide a lie between two truths.
I agree that should be the standard 'greeting' between two SF ships... automatic log/data exchange... but as we saw, this doesn't happen.
Transfer of ships logs and crew reports can be initiated manually (unless the ship is likely in automation mode, in which case, it could be done as you suggest) - though SF ships should be able to fly themselves completely independent of the crew if need be (if pre-programmed to do this).