A few more thoughts on the warship issue: Have the Breen built non-military ships (colony ships, freighters, constructors)? If they haven't, check their difficulty - they may have accidentally been set to "Fool". What is the difficulty setting, anyway?
Also, if you've played this mod before, have the Breen built warships in those games?
I haven't tried it myself but I think the transport trick also works and is probably even more effective than the influence bases. The AI certainly don't like a bunch of enemy transports next to their worlds. It will probably hurt your own relations with the AI race more than the influence bases though as Scanian8 pointed out. Even with the influence bases it's best to work quickly.
Hmm. The reason I wondered if it worked was because I've had several games where two AIs fought a war in space "owned" by a third AI, and it never seemed to harm their relations. As a matter of fact, placing warships (not transports) by AI planets doesn't even seem to harm my relations with them.
Also, just out of curiosity on this topic, how 'paranoid' is the AI about transports by their worlds? The reason I ask is, when I first owned DL, I played on Normal and constantly got "We know what you're doing" messages from AIs, many of whom I never planned to attack. But now on Tough, when they actually do declare war for this, I've only ever had it happen once.
Edit: Make that twice...and this time it was really stupid of them.