I think Fesler has a bolt in kit now too. There is a post on PT about it. Afco's and QA1's combined with remote reservoir.
FWIW, I have nearly the same exact set-up as you, and my car has always been lower on the driver's side by 1/2". Drives me nuts. I wish it was the other way around, can't imagine how it looks with my 225lb ass in it as well. Crooked as a politician probably. I have Hotchkis 2" drop BBC springs in front, DSE 2" drop leafs in back, Koni's all around, Speedtech upper, and stock lower with poly bushings, welded in sf connectors and solid GW bushings. My car is dialed in, square as can be, new spring perches in the back, etc. Just the way it is. If you can get to .5", I think that's all you'll get out of it.
I want to switch to coilovers also, mainly because my car isn't low enough in front and it'll maybe fix my tilt also. Sometimes, you just gotta know when to hold em...know when to fold em...
Getting back to the subframe though. I have my suspicions about it for sure. The column mount doesn't really allow side to side movement, and even if it did, the rag joint is a long, long ways away from those bolts, like 2'. For you to move the rag joint 1/4", you'd literally have to have moved the column over about 2-3 inches (if the rag joint is the fulcrum) which doesn't seem likely. The only way for that rag joint to touch the header, is if you move that frame rail holding the steering box closer. If it was bent up a hair, that would effectively raise the spring pocket, thus lowering the car.
The alignment holes aren't necessarily going to show a slight twist in the frame, they will only prove that it's square in relation to the body/cowl on a horizontal plane.
Maybe take a plumb bob and line and see how far the tips of the frame are from the ground, both with and without the suspension loaded, making sure the car is level front to back and side to side.