The rack is mounted to the front of the cross member. The steering column is mounted to the firewall and floor of the body. Once these two components are mounted they do not move. You then make up the distance between them by using universal joints, shaft and hangers. You do not want more than three universals in the arrangement without using a hanger to steady the shaft. You have a choice of making this configuration up by using double D, spline shaft or round stock, the choice is yours.
If you use a wedge shim behind the bottom mounting holes that bolt the rack to the front cross member, you can lean the top of the gear box shaft back to clear the motor mount. This angle will always be constant and will never change.
If you are boxing the frame, you can weld a mount anywhere on to the inside boxing material. Motor mounts can be fabricated to go over or under the steering shaft. Nothing is standard in hot rodding. Make sure to gusset your mounts, this will add rigidity to the mounts.