Generally I prefer not to align hone an engine, most times it is not necessary. To check, invert the block take your crank and install the bearings in the block, lubricate and then check for crank runout with no main saddles installed or seals. There should be less than 0.002" runout, if not regrind the crank. Next install the main saddle caps and torque, be sure to lubricate copiously. Next rotate the crank and see how easily it rotates, there should be no binding at any point if the crank is straight. In doing this procedure you have just checked your mains alignment and once you remove the main caps you can check for clearance with plastigage etc.
Even if the block has a lot of corrosion a wire brush can remove the heavy stuff and then you can see how much pitting is on the mains surfaces. Scotchbrite works good for this. I wouldn't hone unless the crank was binding or the corrosion was so bad that the surface area contacting the bearings is compromised with pitting. If you end up align honing the block (hardly anyone bores them anymore) have the machinist put in a couple of "tenths" (0.0001") more crush on the main bearings, won't hurt anything. Make sure you install the bearing shells dry, any oil on the backsides will hold the shells off the surface and reduce your clearance.
Most shops only align bore to restore the cam to crank relationship if the engine needs a lot of align honing (pretty rare). Remember anytime you align hone the crank gets closer to the cam which will make your cam chain slacker, there are special short chains for this if you need them. I would spend the money I would spend on align honing and have the engine blocked and decked including the trans face, this way you know the deck heights will be the same and the crank will be square with the trans. All these things are unnecessary if the block is straight to begin with. All the more reason to find a good machinist who takes pride in his work.
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