I took out my O'Brien this evening and had a look. I'm about 50% done.
Definitely the cast doors would have to be removed.
However, several points.
I had forgotten, but looking over this model and the Gold Medal set: it is a very difficult project, certainly beyond even average ship modeler level. To begin with, everything is pretty small at 1/350. It's not a big ship and there's a lot of detail. You've jumped off way in the deep end. That's ok, but realize that there are other kits out there like the Revell Burton Island with PE added, for one, that will be a whole lot easier. There's a reason my Liberty is on the "chill" shelf. This is a very hard model to build.
As for the doors, often PE sets come with parts that are usable at different levels of skill.
The railings, a given. The winches and reels, not too hard to deal with as if they don't work out they really won't be missed by most folks who look at the model.
The doors cast in plastic look darn good. I think the point of the PE set was to make the wood ones look like wood, etc. I would seriously consider leaving them alone as removing the plastic ones is difficult.
They are really an option to replace.