Nylon thread is the normal choice because it is strong and resists the elements well. A problem with nearly all sewing thread is the sizing/lubricant applied to make the thread pass more easily through a sewing machine. Rod wrapping thread should be cleaner, thus causing fewer issues with the finishing steps.
Even if you rewrap the whole rod, one 100 yard spool is plenty of thread. Good deals on new-old-stock Gudebrod thread can be found on eBay. Currently sold brands include Fish Hawk, ProWrap, and Fuji. You can buy either regular thread or NCP thread. NCP refers to "No Color Preservative" thread, because the preservative is already applied. No need to buy an additional material.
You are correct, matching existing wraps is difficult. The following options are in order of difficulty;
- Pick a contrasting or 'matches close enough' NCP color, wrap the male spigots, and finish with z-poxy. The z-poxy should have a minor effect on the final color, probably making it a bit darker.
- Wrap with regular white thread, don't use color preservative, and finish with z-poxy. This may give you a colorless/clear wrap. But clear wraps are not a given without practice and careful control of materials.
- Skip the thread and mount a brass/aluminum ferrule ring on the male section. This would be more than enough protection for any ferrule mishaps. In addition you wouldn't have to deal with thread colors.
- Pull the guides off and rewrap the whole rod. The current guides were finished with epoxy, so removing the guides will take more work that you want. Save this treatment for a rod you really, really want to refurbish.
Tom