You'll have to bear with me, as a novice i struggle with the degree of accuracy required but i am gratefull for your replies.
As suggested tapping by hand did result in a lot of facing to finish the first go but the second was massively better.
I've had a good look and can't see any debris or burrs etc, i gave it a clean anyway and set up a dial gauge.
I've measured the spindle at several points and have found the following
The rear runs out at 0.02
The register runs out at 0.06
The register face runs out at 0.02
And with the dial gauge as near 90 degrees as i can get it a measurment approx 4mm inside the taper it runs out at 0.34.
I can't see how it could be anything other than a bad spindle, any ideas?