Interesting situation, should be quite a challenge. I forsee many hours in front of a monitor scheming the downfall of the AIs, when you should be sleeping
You say that you have max PDC tech... I would say do this:
Get atmosphere converters and convert your planets, and use extra space for research facilities unless it's a real good value (for me, over 130%) in something.
Make a strike fleet consisting of your DUC/Tachyon LCs and a new design with all PDCs. Try to design it so it can easily be retrofitted to the DUC/Tachyon LC, and vice versa, a very fast way to get Legendary Fleets/Ships.
Take on the Jreanar, see if you can't capture a few of those dreadnaughts with your boarding escorts (check in sim first). If you can get just a few, it would be a real boost to your research, and would give you just that much more room to maneuver.
Keep on mining the warps leading to the Phong, step it up if you can.
Pray.
For the question of countering Crystalline weapons, only effective method I know is lots and lots of shields. Those aren't exactly the most damaging weapons, they are only dangerous when the shields are gone.
And about the AI using minesweepers and their speed in deployment... Well, I've never really been on that side of the minefield
If the AI holds true to the form I've seen in it before, you'll only see lone minesweepers come through, not a group. How fast they will come is what I don't know, which is why I say step up mine production if you can.
I'll take a look at the savegame once I get the data files, see if I can't think of anything else.
And how's the Intel of all sides?