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??
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.