When performing main bearing housing bore work on an LS1, LS2, Ford 4.6 or many other modular blocks, the following protocol must be followed.
First, do all of your cap indexing, cutting or aftermarket cap installation and final torquing of the mains.
Next, before boring or line honing, install both cylinder heads and torque them in place per manufacturer specs.
Then line bore and/or hone as usual. I have seen up to a 0.002-in. change in bore dimension after the heads have been removed. This is critical on aluminum blocks used in Super Stock racing, where the bearing clearance can be as little as 0.0017-in.
It’s also worth mentioning that you must hone the cylinders with the head torque simulated on both sides as well. If you don’t have two plates, an old head works fine for the side you are not working on.