I have a clutch of parts for a custom build,

I have a body with rounded neck pocket, however the neck I am going to fit is square.

What is the best way to shape the neck to fit the pocket?

Have you determined the bridge position yet?

If you reshape the neck, it'll sit further into the body, and you'll have to move the bridge back to compensate. You could fill the pocket and rout a new one to exactly fit the neck. Alternatively, leave a gap and cover it with a pickguard or something.
Not placed the bridge yet, was going to get the neck in position first then place bridge.
In that case, what I'd do is make a template of the rounded neck pocket and use that to rout the neck heel to fit.

You can make a template of the exact shape using epoxy putty.
Line the neck pocket with cellotape (so the putty won't stick). Cut out a piece of MDF slightly smaller than the neck pocket. Apply putty around the edges and push it into the pocket to mold it into the same shape. After it hardens, sand down the rough edges and use it as a router template.
Thanks I've not got access to a router easily.

But I've thought of a different approach, I'll take the measurements
of the neck then just add various diameter radii to the corners.

Then trim along each line until I get the perfect fit, which I can then use to
shape the neck.