the second machinist said you can not use standard size pistons after splayed caps are installed because the cylinder needs to be bored with a torque plate installed
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I question this.
I feel that either you mis-understood him or he is wrong. He is corrent in that if you do the splayed caps and torque them down the block will see a different form of stress than it did previously and can distort the cylinders. I can agree with that.
I can agree that it should be then re-honed with caps torqued after finishing and torque plate honed. I can not agree that it should need to be re-bored and re-honed to a different size though. Just re-honing it, should not require new or different sized pistons.
All advice in this thread is good advice in my opinion.
I suggest to keep your 2 bolt caps and to buy and use a main cap girdle on them but to get the align hone checked and re-honed if necessary. You could also just get the 3 center caps repalced to a 4 bolt cap, but I think at the stage you are at the girdle is best bet.
I do not know who has the main cap girdles for the sb chevy now, but I am also getting ready to look for some for one of my similar projects I am on. I heard that Cat is making them, but have not checked yet. Years ago Milidon made them. I know Probe has them for Fords now.
This similar project I am on, has all machine work completed with two bolt caps, and now has a new owner that wants more power from it. lol. I am also looking strongly at figuring something to do with the rear main cap. To me it does not look real strong. I am not sure if anyone is making a billet cap for the rear of these things or not.

Lol

. I just answered my own ignorance by going out in the shop and looking. The GM Bow Tie Rear Main Cap is much more beefy.
Ed