There's also the simple, manual approach: just jettison everything.

I mean, what's the point of dropping equipment when you can load the game where you still have it? Have you disabled save? "I load the autosave", so apparently not. And what does that mean? Have you removed the cargo & equipment from the autosave? In which case, the original question is moot. What am I missing?

Did you extract the zip to its own folder? i.e. you have mods\yamatoshipmod_1-1\yamatoshipmod. Remove that intermediary, so it's just mods\yamatoshipmod.

I'll make an option...

Copy console.dll to your Freelancer EXE directory.

Edit dacom.ini, add a new line with console.dll at the end of [Llibraries] (after flmaterials.dll or jflp.dll).

Now within your game you can press Enter to bring up the chat interface; type help for a list of commands.

park will store your current ship on the current base.

hitch will move you to another base (hitch a ride, since you now have no ship, if there's no ship dealer on this base, or you don't want its ships).

Once you've got another ship, and are back in the base where you parked your old one, xfer will allow you to transfer equipment between the two ships.

I think you could use the extra ships available in Console to do that. Park your ship at the unused base, hitch a ride to buy another ship (which makes no sense given the base is abandoned, but anyway), then xfer equipment between them.

You did not attach the save. I would have thought increasing MissionNum would have done it (Mission = Mission_05 & MissionNum = 15).

JFLP is a patch to fix some things (in particular, it provides widescreen support); it also replaces the original binary-encoded *.ini files with their text equivalents, for easy editing.

The mission files are stored in folder DATA\MISSIONS where you installed Freelancer. The individual missions are in individual directories, e.g. M13\m13.ini.

Using a text editor (Notepad will do in a pinch, but you might like something with a bit more oomph - Notepad++ seems pretty popular) you can edit those files, searching for SetRep (more specifically Act_SetRep). This is the command that changes your reputation with a faction. If you place a semicolon in front of the line (;Act_SetRep ...) it will comment that line out, thus leaving your reputation with that faction unchanged.

Then it's a matter of determining which factions in which missions you want to preserve/comment.

Here's a factions list, relating the nicknames to the name.