I have a 68 with exactly the same configuration - short water pump, driver's side alt, universal bracket, 1-3/4" headers. I got mine to fit right, but only after a lot of aggravation.
I wound up putting a spacer (I used a nut ground down to the right thickness) on the lower alt bolt in front of the alternator inside the U part of the bracket and slid the bracket as far back as it would go.
I also had trouble getting the lower bracket to bolt real solid to the head - I wound up having to use a stud on the front header bolt. It turned out that my header bolts were too short when going through the alternator bracket AND the header flange. The lower bracket was a little loose and my alternator was vibrating.
Sounds confusing, but the bottom line is that I had to mess with alignment a little to get the belt to run straight and true. I don't know for sure that this is the problem you are experiencing, but it wouldn't hurt to make sure everything bolts in solid and is lined up right.
68 Camaro, 383 small block with TH350 trans. 11.98's at 111mph and never trailered.