Hoppy --
My 48 also had vacuum shift assy gone and the change over kit in it. Here's how I adjusted mine and it shifted perfectly after I did this.
1. Make sure you have that 3/4" between the shift levers as per the manual remembering that the spring in between them is just a pressure point to pull against when going into reverse or low gears. When going back through neutral that spring helps push the 2nd-3rd lever back down.
2. After getting that 3/4" measurement, with both the selector rod (the small diameter one or upper rod) and the lower shift rod (the larger one at bottom) disconnected, this is to remember that we are not adjusting the tranny to the shift assy but that the tranny is now king and it will denote where neutral, 2nd, and 3rd gears are gonna be. Pull the shift rod (larger one) up into 2nd gear (you will feel and hear a definite clunk), relax and see if you can pull that rod up just a bit more (usual movement at end of stroke). With that in mind, pull up some more until that slight excess is also out, than adjust the trunion on the shift rod until it just falls into the shift lever. With that done, you are finished with the adjustment for 2nd and 3rd gears. Install cotter pin and just snug the lock nut. With that done the tranny is adjusted to second gear and when you pull down, the tranny tells you where neutral is gonna be and also 3rd gear will be at the bottom on the full stroke. Now stop. Have someone in the car push the clutch all the way to the floor and make sure that the clutch throwout arm is not touching the gearshift rod. If it is, like on mine, than you will have to heat and bend the shift rod about 1/4 for clearance at the first bend of the gearshift rod. If ok, than pull up on the selector rod (small one) as far as it will go and adjust the selector trunion until it just falls into the selector lever. I usually do this last part with the gearshift lever in reverse. Install cotter pin and snug locking nut. Now, shift through gears a couple of times and if it feels good, go for a drive and check it out.
This worked for me and I had a great shifting unit.
Jim.