I'd say pick the ending you consider canon if you want to make things easy for yourself.
There is sort of a non-committal way of explaining away some of stats and effectively "restart" them for the sequel.
You do have a war with the Alliance and whether you resolve it peacefully or beat the chicken soup out of them, you can just mention something like "despite your victory over the alliance, its members still aren't in complete awe of you and indeed some see you as oppressors"
The lizards are even easier. Even if you did manage to get along with them, they're a warrior type race with several factions and probably several of those still aren't going to be happy with you.
While you might have still had a strong war fleet by the end of the Achilles you can also explain that it's not quite as powerful now due several of the ships being in need of repair or upgrades having to be built (And a weak fleet would need to rebuild anyway)
For your multicultural rating, even if you didn't clamp down the iron fist on the alien population, you can state that the war has even made some of the alien citizens uneasy and restless (Resulting in a lower trust) or conversely if you did clamp down, you can assume you released the reins a bit due to the war being over (which would explain the increase in freedom, but still the lack of trust in humans)