#1
Alright - I've had my cheap strat copy in pieces for ages, and having cleaned up the innards and replaced the pups and I've come to put it back together...

However, the A string won't intonate, my question is -

would having the guitar sat in pieces without any string tension affect the neck relief and cause intonation problems??
#2
It won't cause intonation problems, but if you leave the strings off the neck and don't loosen the truss rod, it'll take a day or two (or sometimes more) to get the neck to set properly again. This will cause a bit of fret buzz and action problems but is usually not much of a problem and goes away completely after almost a week.

Tighten the strings a bit and leave the guitar for a day or two and try again.