I am taking off old epoxy and wraps and replacing guides on a graphite fly rod. Once all the epoxy is gone I am planning on sanding the area with 1000 grit sandpaper, is this a good plan and if so how energetic can you be with your sanding?

On blanks with little margin for error, such as most lighter graphite blanks, you do not want to sand into the outer fibers. 1000 grit paper isn't likely to do much damage unless you really go at it, and for some time, but it also isn't going to remove epoxy specks either, without a lot of time and effort.

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If the overall finish on the rod is good and If you are going to put new guides right back where the old ones were, I would not do any sanding. Clean up the best you can using low heat, gentle scraping and denatured alcohol being careful not to scrape off the base finish coat of the rod. I would not take the chance of messing up the finish by sanding the guide areas smooth. Base finishes on most rods are quite durable but thin, and can be easily removed if not careful. You can cover up most flaws by slight guide adjustment, or adding a few extra turns of wrapping tread or a trim wrap. In most cases you can nott tell that guides have been replacef. On the other hand, if the overall finish on the rod is in poor shape, then you can think about stripping/scraping off the finish, wet sanding with 1000-2000 grit wet/dry paper, and refinishing with perma gloss. This is much more time consuming and if you don't need to do it I wouldn't. Hope this helps.
Norm

Thanks Tom, what is the best way to get rid of the residual epoxy specks?

You can usually get rid of epoxy specks by using low heat to soften the epoxy and scraping with you finger nail. You will be surprised how well this works.
Norm