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3 of my rigs have a 6990 each, and they're pulling about 730mhash/s each on OC mode for about 3 months now.
From what I gather though, some optimization can put it higher.

Ideal flags/windows client?

I'll send a few bucks worth of bitcoins to best answer.

Have you tried some of the settings listed on the chart? https://en.bitcoin.it/wiki/Mining_hardware_comparison (https://en.bitcoin.it/wiki/Mining_hardware_comparison)

Yes, but they didn't seem to work as promised when I first set up rigs ages ago.

For example Phoenix with those flags doesn't produce even near 830 mhash/s overclocked (415 per core), yet the guide claims it does.
Well, not a big deal.

What are you clock settings?

A 6990 makes a ton of heat and wastes a good amount of power. The 5970 was more efficient. Anyway I would never OC a 6990 if I wanted it to last a while. You guys have to remember overclocking is not something that is recommended for 24/7 regardless of cooling. If you were gaming it would be fine but OC'ing any card especially a 6990 and having it run 24/7 is just giving it a slow death. I for one avoid any video card that was used for mining, so it may or may not also affect the resale value of your cards.

The best solution for you regardless of clocks is to properly uninstall your current ATI drivers via http://phyxion.net/Driver-Sweeper/Driver-Sweeper/ in safe mode.
Install ATI 11.5b Hotfix drivers + ATI SDK 2.4 and use phoenix+phatk miner with the following flags:
VECTORS BFI_INT FASTLOOP=false WORKSIZE=256 AGGRESSION=13

If help is needed with configuring miner feel free to ask in PM

You should also ensure the card is properly cooled 'cause it's hot as hell.

Flipping the OC switch defaults the clock to 880. 730 mhps sounds about right for that setting. To go higher, you need to overclock past the default 880. Cranking the clocks up to the bios max of 950 should get you about 790 mhps.

Thanks.

However, these flags literally fry the GPU as the other one will instantly skyrocket to 102c.

By using no aggression and worksize 128 it goes just a few mhash lower, but temps stay at 80-90c (well cooled datacenter w/ remote access).
http://s2.postimage.org/ssbgy0jlf/6990.png

Mined with them for months at about 86c with no damage, but I think running at 95-102 and past 900 core clock would prob. damage the cards.
Anyways, this seems like a fool's errand. It's prob. not easy to go much past 730 without further overclocking.

If you know how to bring gpu 2 temp to normal with Phoenix, I'll send BTC.

The best way to gain more hashing power with lower temps is overclocking GPU while downclocking memory while FAN is set to 100%!

My example is:

-Before mem downclocking-

card\core\mem\voltage\temps\fan\hashing speed
5870\950\1200\1.163\90-94C\100%\~409 Mhash\sec

-After-

5870\960\365\1.163\78-80C\100%\~425 Mhash\sec

As I've said I was using Phoenix+Phatk
Yesterday I udated to Catalyst 11.6+Phoenix 1.50
And here are the test results:
http://forum.bitcoin.org/index.php?topic=17379.msg224049#msg224049

UPDATE:
Another thing that I would recommend is to change the thermal grease. I saw some cards where there was so much of it or it had already become dry causing overheating up to 100C with stock settings.

The 1st thing I've done when got my cards after testing them was reapplying thermal grease on all of them (used AC-MX4). After these manipulations I got the temps lower up to 2-5C depending on the card.

Your GPU 2 may just have bad contact with the heatsink or some thermal compound problems.

Just try downclocking your mem and post results. We will find the solution!!!