Yes the holes will be misaligned. And with the Hooligan stiffeners, since they wrap around two sides, the holes will be misaligned on both the side and the bottom of the bracket. The solution is to elongate the holes as need to get the nuts/bolts back on, and then to also weld the bracket to the stiffener.
A die grinder or a Dremel with a carbide burr/rotary file will handle the elongation job.
As already suggested, moving to double shear would be a good idea. Try to get a bracket in bare steel so you don't have to grind off a bunch of powder coating. I know Core 4x4 will sell you a bare bracket if you make a special request.
If you already have an aftermarket track bar with a 5/8" heim end you can make it work with the double shear by adding a pair of misalignment spacers, perhaps some hardened 1/2" washers and a Grade 8 1/2" bolt (probably about 3 1/2" long).