Components

You need to consider if you want to build your guitar from new or used parts and whether those parts are Fender or licensed by Fender (e.g., Warmoth, Allparts, MightyMite).

Personally, I prefer Fender USA parts (even further I really like Deluxe necks) and purchase almost solely through eBay. Fender USA parts are outstanding quality and they hold their value since they are most easily recognized by prospective buyers.

Necks

• The frets are especially nice on the 2007 and later American necks with exquisitely rolled edges. This is true for the Highway 1 and Standard Strats, though I am not a big fan of the large, 70's style head on the Highway 1 necks, they are a great value. All of the more recent American necks have slightly wider string spacing at the nut.

Bodies

• I also go for the Nitro (nitrocellulose lacquer) bodies with the vintage style tremolo. These are from the Highway 1 Strats and are much easier to strip and refinish than the Urethane finish of the other American (e.g., standard, deluxe, re-issue) and all import Strats.
• One of the easiest ways to spot an import body is to look for 1-3 coin sized hole in the body under the pickguard and below the neck pickup.

Tremolo/bridge

• You will need to consider whether you want a vintage style tremolo or the modern two-point style (which cost a little more, and definitely look more modern), as this will dictate which bodies you can use.
• Its also important to note the tremolo requirements. Here Fender uses several types with the most common being the vintage 6 hole mount traditional style. These also come in two primary spacings of 2-1/16″ and 2-3/16″. Most import bodies use 2-1/16″ while American and vintage style tend to use 2-3/16″ tremolo kits.

Compatibility

• You will need to be very mindful of mixing, USA, Mexican, Korean, and Japanese parts from modern and vintage Strats. They are often different dimensions. Same goes for Squires vs. Strats. This get tricky even when buying replacement nuts or saddles, so you will need to do some research to be sure.

Pickguards and Trem Covers

• The pickguard patterns can vary, most are 11 hole. However, the 50s models have 8 hole and the 60s have a unique 11 hole pattern called ‘62 RI (pay special attention to the location of the screw hole just above the middle pickup). Fender bodies come routed for several different pickup configurations with SSS (single/single/single) or HSS (humbucker/single/single) being the most common. Some bodies have one larger trough cavity that can handle any pickup configuration but these provide the least shielding between pickup, and are thus, prone to being noisey.
• There are some differences in style for the trem covers. The major two differences are whether there are six small oval holes for string replacement or one hole the is much larger and giving much greater access (more common in the eighties). The six smaller holes presume that you adjust your tremolo in a conventional manner, so, if you tend to have your tremolo flat against the body, you have to use the whammy bar to align the tremolo for string replacement. The second difference is whether the term cover is just barely larger than the rectangular screw pattern or 3/16" larger.

Tuning Machines

• Vintage Strats and RI (re-issues) most commonly used Kluson tuners. These use 11/32" holes with a bushing press fit into the front of the head. These are great tuners, though perhaps a little delicate. These are fastened to the back of the head with small screws that overlap two adjacent tuners at the same time. It is easy to strip these small Phillips screw heads.
• Modern Strats used various incarnation of the Fender/Schaller tuning machines including some very nice locking tuners in satin or chrome for the USA deluxe models. These use a nut on the front of the head that screws down over the tuner peg. One the back, there are two small locating pin holes for each tuner, that match up with the two pins (pencil lead sized) protruding from the underside of the tuner and ensuring the that the tuner does not rotate.