Cool, hopefully there isn't a large difference then. I'll verify it when I do mine by first comparing the Throttle Body base gasket to the throttle body itself. Hopefully the gasket is the same size as, or smaller than if I use a 2.5l TB gasket, the throttle body. Once I verify they match, or trim it if necessary I'll have a template to measure everything else with. If the friggin' thing is bigger than the bore of the Throttle Body then, I'll have to use some heavy card paper to make a template of my own. I'll put a light layer of paint, or something that will transfer an impression to the intake manifold, on the gasket or the template (now that I think about it, I'll just make my own template from the start!) and seat it on the intake the way it would be if it was being installed - all centered and stuff. When you lift the template, you should get a circle of bare metal that was smaller than the template's bore, surrounded by the paint or whatever. I'll let it dry on the intake and touch it up if need be. I can then grind off the area that didn't get paint on it if there is indeed enough to worry about. The throttle body spacer can be checked in much the same way unless the helical bore starts a distance away from the gasket service. You should still be able to eye-ball it though and see if any metal is penetrating the templates "personal bubble".
I'm under the impression that this problem only exists on Throttle Body spacers that have gadgets and widgets protruding into the air stream like a helix or fins or something to that nature. If your TB spacer doesn't have these gimmicks, you shouldn't notice any difference between your template you made and the bore of your spacer.
Still waiting for my Throttle Body to ship for D-Town (father-in-law picked it up for me as a gift). I will DEFINATLEY take pictures to show ANY difference in sizes that I encounter for you guys, keep in mind though, these measurements/tolerances might change from year to year and stuff. Throttle Body spacers are different between manufacturers, too. I'll let everyone know what I use when I get all the parts.
If anyone else does a TB swap, they should take some pics of the job while they do it and post them in the mean time. Be a little scientific and try and find out just how much of a difference there is between the 4.0l Throttle Body bore and the stock intake manifold.