First of all the forward relief on the neck is usually quoted by Fender in the realms of 8-12 thou depending on radius of the neck and typically around 10-12 thou. However if you read other books they will suggest as much as 1/64 of an inch (The Guitar Handbook by Ralph Denyer) I find a bit more relief is what I like.
The string height for vintage strats is qouted around 4 - 5/64s for 7.25 radius but if you set all the strings to the same height I do not feel that gives good sound. I prefer to set my string height around 2mm on treble side rising gradually to around 2.5 mm on bass and this I think allows the PUs to come up a bit higher on the bass side and help project the sound across all strings better especially for single note lead playing. I think to myself why did they stagger the PU pole heights the way they did and then slope the PU down on the bass side ? Seems to me the PU should be a bit closer to level which is why I feel the bass side needs to come higher on the strings permitting the PU to have less slope bass-treble. This way I get nice sonorous bass notes and full trebles with good output across all strings for lead instrumental style playing.
Generally as you flatten the foward relief you need to raise the bass end more and I think there is a point where a good balance is acheived between the two.
I have a strat with a Poplar body and a vintage with Alder and the Alder body is much better sounding certainly accousically. But with good setup I can get just as good a sound from the poplar body when plugged in and played leading me to conclude that setup is vital to get a great sound.
Obviously intonation needs to be set right and I found recently when I checked a strat it was out and after resetting intonation it sounded much more alive and less dull as if the relative tensions in the strings had changed in setting the intonation correctly.
PU height again Fender gives measurements here but I find my best sound projection I am very different in heights on treble and bass side. Also just a 1/8 of a turn on either side bass/treble changes everything and sometime needs to be spent getting good projection and sound balance across all PUs. People have told me I got one of the best Quacks from my middle PU and I know it is in the way I set the PU heights and slopes (and also the way I play). My plectrum choice also affects this.
I played several strats at our club once and was told by one guy that I sounded the same on all of them ! So maybe as they were all set up different it was me ! I dunnoe but I had another friend who was not quite getting a great shads sound and a few of the above adjustments bought that cheap squierer into the realms of the right sound.
So my point is a good setup does affect the guitar sound and improves the tone. Low action is not best for lead instro work either as it thins the sound too much.
My opinion of couse but I hope it helps someone as I have spent ages looking into how to get the best setup on my vintage strat and belive I have found something that works for me at least !


