Motorhead,
(Hi), get the pistons prior to the work being done on the bores, as most people have said. That way you'll get it exact. Just so those who didn't take this approach don't start panicking(!), a lot of machine shops will overbore before getting the pistons. I've had plenty of experience of this as many, many people didn't change their ign timing/carburation when leaded fuel was phased out here. This resulted in a lot of holed pistons & ruined bores. Usually people were in a hurry to get the motor back together, as it was their daily rider, so they'd order the oversize pistons & get the bores machined while they waited for them to arrive.
A new piston & a fresh bore will each have an upper & lower size specification. A good machinist will bore to the size that will give the minimum clearance for a piston of the greatest spec'd size. So when the engine is built you could have the ideal clearance or anything up to the maximum allowed, if the piston is within spec. This isn't the best way to build an engine as the clearances could be all over the place. For an engine that's not being balanced & having the chambers cc'd, etc, etc, it'll run OK & do it's job just like an engine off of a production line (how many manufacturers bore to the piston size, degree in cams, etc?). The problems really start to occur when the piston sizes fall out of spec, but you'll check that prior to fitting them :) I know of many engines built this way that have clearances that are greater than ideal (the minimum) & they run just fine. But the engines that have been carefully built with all clearances as close to ideal as possible tend to run just that little bit better & smoother & will hopefully have a longer life expectancy. I'm not talking about engines that have clearances well out of spec (they'll either sieze up, burn oil, lose compression, have piston slap, have high crankcase pressure, etc), these are engines that have the piston to bore clearances varying within permissible specs. If the piston to bore clearance is outside the limits then it shouldn't be built with that piston in the bore. This is all assuming that the machinist knows the correct size to macine it to & doesn't take it out too far - then you will have problems.
Don't forget that a lot of times oversize pistons are fitted to repair an engine that's been damaged & will be used as a grocery getter or daily driver by somebody who's only interested in getting from A to B. Any slight loss of power, or small amounts of oil being burnt, doesn't matter to the owner, as long as the thing runs OK.
For performance use (or to just build a good engine ), always bore relative to the measured piston size. If not, then find a friendly piston supplier & selectively fit pistons to the machined bores so that you get as near to the ideal clearance as possible (I know of one manufacturer that definately did this in production). If you have to, err on the loose side rather than the tight side (loose enough to cause piston slap is far more than erring!). Use the clearance specified by the piston manufacturer for that piston & also check ring end gaps are correct.
And then weight match them all (fully assembled with rings, wrist pins, etc) :)
:cheers:

 

With all the attention to bore size/piston fit, don't forget about ring end gaps.
A set of .030 over rings may need some "fitting" in some cylinders.

Installing the rings without checking each ring in it's intended bore could lead to failure.