Don't overbore unless you have to. If you have standard bore pistons and your cylinder walls are in decent shape there is no need to overbore. I had to because my 1st and 2nd cylinders had pretty big scratches on them.
The LS water pump and timing belt will work fine. Are they pretty new? If so then just use them, if not then I would go ahead and get the VTEC units instead.
As for the ARP bolts, use the same sequence as stock and use the torque specs that came with the studs. I can't remember them off the top of my head.