Most of the vintage value is in the neck. I've bought vintage bodies for $300 and vintage pickups for less than $150 each, but when it comes to vintage necks, a pre-cbs neck in good condition with original tuners usually warrants at least $1200.
If you're looking to spend $2500, you can probably find a fully vintage refin JM from someone on the OSG forums, or maybe on ebay if you keep an eye out, like this one: http://www.ebay.com/itm/Vintage-Fender- ... true&rt=nc
Also I wouldn't get too hung up on vintage pickups, they seem pretty over-valued these days. I've done tests with customers between a 59 JM, a 64 JM, and a 63 JM with Pickup Wizard pickups in it... and everyone prefers the pickup wizard pickups! I prefer them too, which is why they're in my 63 JM


