Machinists please help

As previously mentioned, what about align boring mains? As the main bearing bores are typically used for deck height reference, it seems logical to begin there. Also consider ARP main bolts when you buy block hardware.

Are you buying a complete rotating assembly "stroker kit"? Best to have all parts on hand prior to machine work on the block for a few reasons. First, most machinists prefer to have the pistons on hand so clearance can be set and an appropriate finish for the rings can be applied. Second, depending on crank/rod combo there may be clearancing of the block needed. Best to do this before the final washing and assembly. Third, in order to properly set deck height, crank, rods and pistons must be on hand for mock up.

And finally there comes the "sticker shock" aspect of the build. This stuff starts costing $$$ real fast, and to be honest a stroker is not exactly a cheap engine to do right. If you have $5000-6000 to spend on the engine, plus a couple thousand more for various supporting upgrades to your chassis,then by all means dive right in. BUT since you seem young and on a budget I would have to ask why not just rebuild a 360 and drive the car? You could have a stout 360, exhaust system, converter, front end kit, brakes and maybe even a coat of paint on the body for what that stroker will finally cost you. Something to consider...

Sorry if I didn't tell you what you wanted to hear, and I don't mean to insult you or your build. But you've asked for an honest opinion and I've given it.

BTW clearancing for timing chains is typical of fitting a double roller on a small Chevy, especially early small journal blocks and probably wont be an issue for you.