Is there a recommended way to center your handlebars?
It sounds as though you have drop bars, and one of your measurements is to the brake hoods. Since those are independently attached to the handlebars, that measurement only tells you that something is off, not what it is (you have two measurements and three unknowns - the bar position in the stem, the left brake level position on the bar and the right brake lever position on the bar).

I assume there are no markings on the bar, and no bulge where the bar thickens to 25mm from 22mm, otherwise you wouldn't be asking?

I suggest loosening the stem off and making a mark on the centre point of the bars, measuring from a point that has a sharp edge. If the bars are new the end of the drops is good, but on old bars one or both end is often bent a little. Even 5mm makes a noticeable difference here. If the bars have been taped the tape will also affect the measurement, which is why the bar end points are good. 

But regardless, the next best way to measure is from the inside of the forward-swept part of the bars. Get a ruler that's longer than the width of the bars and place it on top of the bars, at 90° to the bike's long axis (across the handlebars). Line it up parallel to the bars, so that it's just in front of the cross part. and the same distance forward on both sides. I find that lining up the forward edge of the bars and the back edge of the ruler works well. Then measure off the forward edge of the ruler, since that's on the straight parts of the bars. 

Here's a quick top view:



Ideally your bars will not curve this much, or you'll use a wider ruler :)

This lets you measure the exact width of the bars. Halve that, and measure in that far from one side. That's the centre :) Now make a mark there, or better still, mark the ruler and centre the bars in the stem with it in place. A couple of rubber bands can be used to hold the ruler in place while you do this - put them on the rule, put the ruler on the bars, pull a band under the bars and over the end of the rule. Repeat for other side. Now wiggle the bars in to position. Test ride, and make sure it feels right.

Mark with a permanent marker both sides of the stem so you can line it up easily next time.

Also, now if you repeat your measurement to the brake hoods you can twist one or both on the bars to get them symmetrical. If you prefer them that way.

This also works for most other curly bars.