OK so, you have mono leaf perches with no hole in the center, you have multi leaf springs but the center bolt has been ground down to only 1/4" in height, You have an insulator in the perch on top of the spring with a hole for the center bolt, Once you loosely assemble the springs, axle and shock mounts/lower plate, you will position the axle so the pin is through the hole in the plate. Once you tighten it up that is how the axles are aligned. That is how the stock mono leaf springs are assembled. The multi leaf spring is a better idea with the hole in the perch. IF, only if, you can put a hole in your mono spring perch without drilling into the axle tube, that would position the axle correctly onto the springs. I think it is a good idea to get rid of the upper isolator in the perch and have the spring riding right against the metal of the perch. The rubber isolators are there to help the rubber bushings in the spring eyes and shakles reduce vibration and harshness from the road. The rubber isolators can also allow movement of the springs in the perch which can be a cause of a broken center bolt. The rubber isolators can also compress enough to alow the center bolt to make contact with the perch if there is no hole.
So my suggestions to properly align your springs and axles are: Drill a hole into the center of the perch, if possible, to align the axle to the perch. You may be able to drill in deep enough with a 1/4" drill or 5/16" drill then finish with a proper size drill that has had the point flattened out if neccassary. Then install without the rubber isolator; If drilling a hole in the perch is not an option, make two isolators out of steel the same legnth as the perches and slightly thicker than the height of the center bolt. Place the steel isolators over the center bolt and align the isolators in the perches as you assemble the axles and springs. That will position the axles in the correct position on the springs; Retorque the ubolts after the first outing then after 50 miles then after 500 miles. Just torque to spec, don't over torque. Loose ubolts may cause leaf or center bolt breakage.
Can you post a photo of the kit you have to convert the perches to multi leaf?