The safety release cables should be inside the top channel, along with the equalizer cables. If they’re routed properly, they won’t foul.
The long threaded rod goes through the columns, front to rear, just above the equalizer pulley, at maybe 1:00. It’s shown, but not talked about in one of the prior illustrations. If I recall, it’s sort of a safety guide to keep the equalizer cable in the pulley shive if something goes wrong. You can’t thread the cable if that threaded rod is in place, as there’s not enough room to slip the cable end through the gap.
The instructions are actually quite clear….for someone who’s assembled a lift before. For a rookie…not so much.
The best thing you can do is search online for a few YouTube videos, even if they’re for other brands of two post lifts. A few hours watching videos will help immensely.