There are different styles of bushings.  A picture of the bushings you are working with would be a big help.  Then we could help you get it right.

Or, it might be as simple as the wheel has shifted fore or aft, or up and down while you had it apart.  It is easiest to install the bushings with the car at normal ride height.  If the wheel is hanging down, it will try to reposition the strut rod at a different angle. 

When I install new bushings, I typically remove the strut rod from the LCA with a jack supporting the LCA at normal ride position.  Install the bushings loosely on the rod, then reinstall the two bolts at the LCA.  At that point, you can put the weight of the car on the front wheels and everything will align correctly. Or, at least as correct as an old Mustang is ever going to get.  Then tighten the bushing.

IF it came apart OK, then it is probably OK to go back together.  Just reposition the LCA until it goes in.

Remove the strut rod from the LCA.  Insert the bushings where they belong and install the nut loosely. Then use your floor jack to lift the LCA up into position and slip the bolts of the strut rod into the LCA.   You may have to move the wheel assembly front to rear or vice-versa to get the bolts to line up.  Up the LCA is up too high, they won't go in.  If too low, they won't go in.  Play Goldilocks and get it so it mates up "just right".