I'm currently rocking the Kenny Brown version of the Cobra IRS, which is just an OEM core that they put in their jig and re-weld all the control arm mounts as well as weld up the flat subframe mounts for the rear.
I don't think there's really anything that can be done to increase stiffness, and you'll get a sense of that once you see an IRS subframe up close. For one, the tubes are massive in circumference, much more diameter than any roll cage tubes. And the swaybar mount area that connects the upper and lower part of the subframe is incredibly beefy. The thing is rock solid. I for one don't think there's any amount of power that can pretzel this, as surely it is not the weak link.
I wouldn't worry about squaring up the IRS subframe to the rest of the car. Like I said, when these things were made, it was by a billion dollar company (Ford) and I've gone through two of them - both have held alignments perfectly (with modern machines that use the laser reflectors). You should have no worries. Unless you are unfortunate and someone sells you one from a car that was hit in the back and they didn't disclose the damage, that is.
I'd worry more on making sure the front subframe of the car is squared up with the rear torque boxes, with plumb bobs as outlined by the Maximum Motorsports tutorial. Once your IRS subframe is installed and torqued down, all that's needed is just the 4-wheel alignment and presto.
