Should the caps+girdle be installed when measuring the bores? If so, can the block be supported at the ends with blocks of wood (as opposed to a stand), without distorting the readings?
Don't take this the wrong way but your inexperienced measuring techniques and the block's temperature are going to have a greater effect on bore measurement than bolting the main caps on.
In this case it might not make a big difference in measurement if the mains are on and torqued or not. It is a very good habit to have everything torqued to spec before measuring and machining. Not all blocks distort in the same way. I have seen some 4 bolt V8s distort the lower bores severely when the mains are torqued down. Some inline 4s don't care.