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If it fit before the new header... then yes, sounds like you have to trim the wood. In my case, I was assembling a new header with a windshield that I assumed was for a 1930 Model A. Same issue, windshield would hit the gas cap. After a lot of pain - I determined my windshield frame had a 1929 hinge on it, instead of a 30-31. It drops the windshield down... Look at the pictures in Snyders catalog to see the difference in the upper hinge.
Good luck