I have the Jake's 3 inch spindle kit on one of my Club Cars. I lifted the cart as I wanted 205-65-10 tires on the front also. I have no issue in tunnels.
I also have 205-65-10 tires on the rear of my second Club Car. I have no issue with the wheels rubbing. I only mention that thinking that you should check your leaf springs to be sure they are performing as expected.
If you do carry a heavy load, it is possible heavy duty leaf springs will solve the issue. I would call Jake's and describe what you seeing and they should be able to provide some guidance.
Club Car | JakesLiftKits.com