On my rig I kept bumping the lower studs on rocks and snapping them... which ended up really biting me on the last RoundUp. I just went to 10mm studs, hoping for no more broken studs. After drilling/tapping for the 10mm studs, the stud alignment was slightly off like you're describing yours are now. I ended up just putting some nuts over the ends of the studs to protect the threads and used a small sledge to knock them into alignment. Worked pretty well... and hopefully the 10mm studs are big enough I won't be breaking any.
