[tbirdtbird]

hmmm.
If you truly have .003, you are farther ahead than most.

What is supposed to happen is that the machinist is supposed to bore to the specified dimension, for example 4.000 (this would be .125 over of course).
The pistons are supposed to arrive in the box at .0035 under. But they never do. Sometimes the piston dimensions are not the same amongst the 4 new ones you just bought.
So, you mic each piston, and if you need more clearance, then you use your hone to get there. This implies that you have an outside mic that will go to 4.000 and an inside mic set that will go to at least 4.000. If ya wanna build a motor ya gotta have the tools.

In short to do it right you have to mic everything, and not just shove the pistons in the holes without measuring, which is what we see all the time.

I have honed cyls while the engine and crank were still in the car but you have to take extraordinary steps to protect the crank and its journals; and you have to wash the cyls and block walls down very meticulously. A royal pain.

If it were me, I would remove the plugs, buy or borrow a bore scope, get a good look at the cyl walls. If they are not scored, then re-scope every 1000 miles or less.
Were your pistons old school long-skirt (prolly I am guessing). More risk if they were.
When tight clearances seem to show up is between 500-1500 miles.

Whatever you do, keep the radiator filled and do not allow the engine to overheat. Be sure the timing doesn't get retarded; a late motor will run hot as hell.

When you use the scope, and if there are no score marks, you will feel better; then just re-scope every so often.

Modern day clearances are in the neighborhood of .002, which is waaaay too little for an A. So you have to avoid modern day shops that do not speak Model A. Also, I have seen new A pistons come with a slip of paper which says to set them up at .0025. Sorry, this is wrong.

Good luck. Scope and get back to us