If it were me, I'd pair them up as best I could so and then assemble them with a permanent grade threadlocker to seal the threads and hold the pair together in proper alignment. A downside might be removing the valves later if necessary for later maintenance. I think the stems are short enough to reinstall them after the heads are assembled, but I'm not positive. To make yourself feel a little better, you can make a fixture to pressure test the combination after assembly a lot quicker than re-machining all the cylinders especially if you've already honed them. The pressure test is a good idea in any event. I tested my head assemblies this way. - TerryI believe you are all correct, thx for pointing it out. I may need to cut more cylinders if this turns into a bigger issue. For now I am moving forward with cylinder head work. I am thinking about some options that might allow use of the drilled cylinders. If I match them up at a certain point it may address this problem.
Keep in mind that Ageless recommends torquing the heads to the cylinders really tight to prevent leaks. He doesn't recommend the use of Loctite with the recommended assembly order due to fears of it setting up too quickly under the heat of torque. But it may be your best alternative so long as you select the parts to mate without requiring a really stout torque and instead allow the Loctite to do the holding and sealing. - TerryI like the pressure test idea. I also like the matchmaking idea for early on for the cylinder/heads. I just ordered the head aluminum. I think I will match them up early so they are matched sets. I made a test block for the cylinder head threads. It turned out pretty good with decent thread fit.