Yes, the drag and drop aspect of the custom form builder is "one field at a time". For my (oil and gas) clients, who have 2000+ custom parameters behind each project, like you, I found the process tedious and time consuming. So, we created our Update Category solution, which lets you:
generate the "definition" of an existing custom form into an Excel Format using our Update Category Generator
manipulate that definition in Excel, including adding, deleting, and reordering fields, changing formulas, and so forth
upload the changes using Update Category
As long as the same fields are present, all the existing data is preserved; and in the interest of protecting your data, it also warns you if any fields are about to be dropped.
In addition to saving an enormous amount of time, should you choose to save the Excel Files, it has the added side effect of "archiving" the variations made to a custom form over time.