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Let me see if I can help. Just to establish a few details, are the shafts flush but not protruding inside the U-joint yokes? It is important that the pinion shaft on the rack unit is flush with the inside of the lower u-joint. If it protrudes into the u-joint it could be binding but if it isn't flush it could be causing too extreme of an angle on the upper u-joint.
Also, are any of the setscrews hitting anything? The lower setscrews on both u-joints are areas to look for that. If all of that checks out you can try to adjust your steering column by moving it to the side a little. Depending on how the body sits on the frame of your car you may have to angle the column so that the end of it points a little to the outside of the car (rather than parallel with the centerline of the car).
Let me know if this helps or if you have more questions.