This reminds me of my car. I have rub on one side also. I measured my subframe and found one side to be 1/8 off. I also didn't know enough at the time to measure that its square. The front frame horn is bent in on one side (didn't know until I was putting it together). The bumper and hood don't fit right and it drives me nuts. I also run big 235/15 tires so no room for error.
I have considered getting a brand new OEM frame for around $1000 bucks but I would have to go through the panel alignment like you said. But I don't think the panel alignment would be all that bad. Three of the 4 points are all on the firewall piece. If you keep your shims all organized you shouldn't have much problem.
Its all the other crap with changing it out that really make me shudder. gas and brake lines, swap the motor, do the "Guldstrand" mod again, swap the suspension.
