So, I some how managed to do some Breen missions before the min rank, and I picked up some of the Breen set for my ship - but only at Captain Rank.

They say max - one per character...so does that mean I can't get them again when I can do the missions at 48?

No, you can get them again. It means you can only have 1 at the time in your inventory.
So if you sell that one to a vendor you can get a new one.

You don't have to vender them first. if they are a mark VIII for captain and you are a Rear admiral now then you would pick up the Mk X version and the Mk XI at Vice Admiral.

The mark value is taken into account in the Unique item tag. It is also taken into account when you mix and mash mark values in the same set and unless they are the same mark value you will not get the set bonus.

Which is horse crap. A player should get the bonus of the lowest Mk equipped.

It is crap but IIRC the set bonuses don't scale with Mk level (all Mks have the same set bonuses), so really you should just get the benefit from the enhanced stats of the higher Mk base item. Still crap though I agree.