It's likely lawful to do what you propose ONCE and sell the guitar as a used, customized Fender Stratocaster. But you cannot lawfully do what you propose as a business enterprise. It's called "reverse passing off."
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Claiming you produced a product you did not can be a trademark violation called reverse passing off. Consult with an attorney to discuss exactly what you want to do.
Probably yes, you can proceed as planned. There's no general wrongdoing in modifying and reselling a guitar. Potential problems arise depending on how much you modified the guitar and what you say about it. The test is whether the modified guitar is "substantially different" than the original. If your modifications (in the opinion of a court) render the guitar substantially different than the original, you'll probably be fine even if you claim the guitar as your own product. Safer, though, you can avoid any problems by simply being honest about the guitar: advertise it as a modified Fender. Problems would arise if you were to advertise a barely modified Fender as your own product. That would be reverse passing off.
I completely agree with the other attorney answers. Just to build on their responses, trademark rights are not limited solely to brand names such as Fender or Stratocaster. There is also such a thing as trade dress rights which can protect the way a product looks, which may very well exist with respect to the shape of the Stratocaster guitar. Thus, simply removing the Fender Stratocaster branding would likely not get around these issues. Therefore, as Mr. Ballard advised, the best you could probably do would be to sell such a guitar as a used, customized Fender Stratocaster. However, you should still consult with an intellectual property attorney so that they may better advise you based on the specifics of your situation.
The above response is general legal and business analysis. It is not "legal advice" but analysis, and different lawyers may analyze this matter differently (i.e., reasonable minds can always differ), especially if there are additional facts not reflected in the question. I am not your attorney until retained by a written retainer agreement signed by both of us. I am only licensed in California. See also avvo.com terms and conditions item 9, incorporated as if it was reprinted here.