I have friends that re-do the masts and yards with brass tubing or rod stock even if they are not modifying the kit. They do not like the wimpy plastic masts and yards because they bend too easily when rigging. I use the K&S rod or tube stock if the kit masts are badly warped or too weak.
Rigging is something else. Each shipbuilder I know does things a little differently. Personally I use the transparent monofilament to lower visibility, and swear, every model, that I will never use it again because it is so hard to use. Yet I have found nothing that looks as good when finished.
Whether modified or in areas you are using stock parts, drill holes for attaching rigging whenever possible.