why wouldnt you want to get oversized pistons and bore your block while youre rebuilding it? you should also machine the deck of the block to make sure youre working with a perfectly flat surface. youre also goin to have to get the rod's refitted for the new bearings, along with all other bearing surfaces. while everything is open, i'd suggest having the rods bead blasted/polished for additional strength. id also have the machine shop figure out the finished weight of the rods/pistons and have them balance out the crank. have them balance it to your redline, this will help you gain longevity out of your bottom end.
also, have the head r&r'd. if you dont, your simply inviting problems. run a ctr intake bumpstick with just about any exhaust bumpstick of the oem variety. also have them 5 angle your valve seats, re-cut the valves, and heat the springs to gain stiffness out of them.
also have everything in your intake line cleaned and matched to each other if thats the least you do. id have the TB polished, the IM ported/polished/matched, and the head shipped off to endyn telling them what the head is goin to be used for build wise, and everything i am gonna run with it and where i wanted my power....which should be mid powerband with more emphasis on torque so you can run a different gearbox.
ctr pistons are over 1 ounce heavier than b16a's. the only "advantage" ctr's have is that moly coating.
an ls waterpump will spin faster than a b16, there is a 3 tooth difference. some say you cant use it (the ls), it may be true, so there is a heads up.