I understand how you wear out frets, but I don't understand how you wear out a neck. People love the feel of an old worn neck on a 50's tele, why not a 90's Squire? Are the screw holes worn? Has refretting damaged the fingerboard?
If pickups are the nervous system of your guitar, the neck is the soul of it. You can get a first rate neck from Warmoth or any of several other sellers for about $200. You can get a cheapy from GFS for $50 or a respectable one for $90 from International Luthiers web page. The thing is, it will never feel the same. There is a slim chance you will like the new one better, but chances are that you will not like it as well. While mounting the new one is easy, getting the thing set up just so can be tricky. I would say, spend $45 on one more refret and save your real money for a new guitar. Then save this old friend for a back up guitar. Pull it out once in a while and enjoy that "well worn jeans" level of comfort.