56 3100 Front fender to cowl seal - tough fit

[BS Stuff]

In working on this 56 Panel truck for my buddy - I am trying to use all the parts, etc he bought over 10 years ago. So after fitting aftermarket door to cab, and then fine tuning good used fender to make gaps look good, etc - I am having issue after installing the seal on fender at rear of fender to cowl.
I checked with GM assy manual and see it goes behind the welded reinforcement that goes top to bottom on inside of fender - at the rear most portion if you will. Issue is seal so new and fat - it will not allow fender to sit where it was fitted - which means door hits / rubs when opening it. (Or not opening but checking for interference).
Question is - does everyone put those seals back in or leave them out?? I was debating trying to remove material off the seal and if still issue - then removing all together. Getting the 2nd fender ready so do not want same issue.

Any ideas?? Thanks in advance !!