Building your own strat

Is intonation going to be a problem assembling your own guitar? I was informed that intonation adjustment is not as simple as checking tuning at open string and at 12th fret. There neck intonation and also body intonation. Not quite sure what he meant. Any comments on this part?
 
For those intersted in DIY strats projects I have the following items up for grab:

ORIGINAL FENDER JAPAN 57 (8 hole s/s/s 6 screw bridge style) STRAT BODY ONLY $200

ORIGINAL FENDER VINTAGE USA STYLE 6 SCREW BRIDGE SET COMPLETE $150

57 1 PLY WHITE PICK GUARD S/S/S - STEWART McDONALD $20

ORIGINAL FENDER USA 1 PLY WHITE 6 HOLE BACK TREMOLO COVER $10

ORIGINAL FENDER USA WHITE VOLUME /TONE /TONE SET $10

sms 96909640 - get em while stocks last
 
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