I found a work around for the door control rod misalignment you might try. The YouTube video linked below recommends replacing the 47 to 54 door controls with ones from a 1964 to 1966 C10. Available from the usual vendors. (Classic Truck Parts # 18-831 and 18-832) These will put the mechanisms in the door channel and allow the door panel to fit better. The inner door handles still work in the correct direction.
47-54 Chevy Truck Doors Tech Tip #HotRodDad #techtip #chevy3100

1954 Chevy 1300 engine 235 (1959)
1955 (first series) Chevy 3100 engine 261 (1957)
1927 (other brand) Model T- engine 327 (1968)