If for a moment we assume this problem is the same as the DC/Faces set and if we take it that Laserman was right about that problem and that the misalignment is constant. Then I think I may have a solution.

I have just found a filter for FCP that should let me make either the upper or lower fields of a clip transparent. If I was to set-up a timeline with two video tracks containing identical video clips (LD Sides + VHS Clip) and then apply this filter to the clips in both tracks but setting the clips in one track to make the upper fields transparent and the clips in the other to make the lower fields transparent then I should be able to adjust the vertical position of the clips in one track to try and bring the two fields back into alignment.

I will give this a try when I get home tonight and post back with the results. :)