You are on the right track. Given the lack of connectoin between your hinge pillar and anything below the dash you will need to get it located correctly before getting it secured to the rocker panel and front cab mount.

Replacement panels are not a very good fit typically and should not be used to locate the critical parts (such as the hing pillar). Rather locate the pillar and then massage the panels to fit.

1949/50 3600 Project
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