I had a similar problem with my build. I did not chase the threads in my Stealth Heads, just threw them on when I was ready. My block was decked for zero piston clearance and that changed how the aftermarket intake aluminum manifold would fit. I ordered the correct thickness intake gaskets to make everything work, but as many know bolting up the intake in this situation with the under-pan, two gaskets, and the manifold can be a pain. Anyway, I did not like how the bolts felt going in (had to force a couple), so I pulled it apart to check everything and there were many shavings from the intake threaded head holes in my lifter valley (and lifters). I had to flush and clean and then I chased the threads and put it back together. Then when the engine was all finished I put cheap oil in it, spun the oil pump and drained the oil as a flush. I have not started this engine yet, but I think its ready to go.
Also, I have read that some of the Stealth heads need to have the push rod holes clearanced. My did not need it.
