Hold the phone.
If your customer will accept pass/fail functional gaging pins will be OK. Many will not depending on criticality and application. They may insist on actual measured size, that is, quantitative data: size of the hole, roundness, cylindricity, location etc.
It is possible for a hole to measure within tolerance and yet reject both limit gages. An odd number lobed condition is almost almost undetectable checking by diameter only and a circular interpolation is particularly vulnerable to this kind of error along with other errors like back taper, hourglass, barrel and other wierdness depending on the concenricity of the cutter flutes to the spindle axis..
Regardless circular interpolating a bore with an end mill is subject to too many sources of error to reliably hold a +001"/-.000" tolerance. An exception may be when the hole has little significant depth; a rabbet fit for example.
Your best bet is to rough with the end mill leaving 10 thou stock and bore to finish. A bored hole will far more likely be acceptable than one circular interpolated.
I suggest you check size with a mike and a telescope gage ir dial bore gage. Cheapo eBay $36 bore gages aren't that bad if compared to a reference bore of known size, a setting ring, or stack of jo blocks with the setting attachments. A good dial indicator is the saving if an indifferent quality bore gage.
Don't discount telescope gages. In experienced hands they are damn accurate. I've used telescope gages to work to 0.0001" checking on the micrometer provided the bore finish is up to snuff.
I suggest any who sneer at the accuracy attainable with telescope gages should learn how to use them. It's a skill and that takes practice and technique.
Here's a start:
http://www.wikihow.com/Use-and-Read-a-Telescoping-Gage
http://bbs.homeshopmachinist.net/archive/index.php/t-27178.html
http://www.youtube.com/watch?v=SmXfGan_NXQ
The guy in this calls a telescope gage a "snap gage" which aint orthodox in most parts of the country but he shows the correct way to use it. Taking an accurate reading from the gage with a mike requires a careful touch, some back and forth to max the reading, and a little patience. Take several readings but do not average them. D=Measure blind: don't look at the mike. You can "wish" a couple of thousandths one waay or the other so easy you'd never credit the phenomena. Reject the extremes. Those that cluster within 0.0002" are the ones to take to the bank.