The issue with the pushrod guides occurred in my Vista also and I had to experiment with each pushrod to determine the correct tube for each. I still had to add 2 mild bends beyond the exit to allow the rudder pushrod to work freely. The 3rd tube is likely for the antenna of those who still use 72 Mhz radios.
If you chose to shim the wing, see that the wing rests solidly in the saddle.