I would suggest reversing the last two steps and set your pickup height before you set your intonation because if your pickups are too close to the strings, the magnetic string pull will throw off the intonation making precise adjustment difficult if not impossible.
Like I said in my post, if something looks obviously off I'll adjust that first and I've done enough setups to tell if things seem odd when setting the intonation. Having said that, I probably do actually do the intonation last after the pickups. I think I wrote it down in the wrong order.