As far as the the rear end tracking issue goes, 1/4 inch is not that big a deal, it's only 1/8 per side which I wouldn't worry about...The problem now is not the tracking of the rear end as much as your wheel base, once you have all the sheet metal bolted in place...about a week ago you mentioned that getting the sheet metal on with acceptable gaps was your main concern and by the sounds of it, we are pretty close to that now.
What is happening is that we are, for lack of better terminology, splitting differences when we align sheet metal this was...we didn't have a choice because of the rear frame rail issues not allowing us to align the front frame to the rear frame. When all the fenders cowl, rad support etc. are on and your happy with the gaps, you can bolt down your front sub frame. That is when you check for wheel base and that will determine either front or rear tracking. I hope I'm explaining this in an understandable way.
Are you shifting the entire sub-frame over 1/4 of an inch or moving it at an angle?