When installing your overhauled cylinders install the rocker shafts BEFORE you install the cylinders. You have room to move the shafts after the cylinder base nuts are on to install the rocker arms. I just went thru this on my HIO 360 c1a
Not only that, but if you're just changing cylinders without splitting the case, remember to pull out the hydraulic lash adjusters and purge out the oil...