I think I centre-drilled mine, and used a tailstock centre to stop it flapping about. I think I also had cutting issues, until I used Jason's suggestion of a DCGT insert. In the end (after two failed attempts) it was very easy to do.
Someone mentioned not turning the end down at all, and enlarging the hole in the valve chest to suit (I think that's what they meant), but you can't really do this because the middle of the rod needs threading, and so the turned end needs to be just a bit smaller diameter than the die that you'll use to do the threading (ie the turned diameter has to be equal or less than the root diameter of the thread). I made this mistake first or second time, and had to start again – again. If you didn't turn the end down, you'd end up with a threaded rod going into the valve chest guide hole.
I think someone also mentioned when I was having issues with this, that another way around it is not to turn down or thread the rod at all, but drill and tap the side of the square brass valve plate so that you can slide it along the rod and lock it precisely where you need it with a grub screw. It makes adjustment much quicker and easier. Using that method I guess you can use the same diameter holes in the gland and and the dome end of the chest.
Only reason I didn't use this method was because I wanted to build to plan, and didn't want it to defeat me!