I get what your saying. You have most of the stuff, so learn as much as you can. I appreciate the manual, but it's to just get you by.
Post up the actual size of the piston you are going to use. At this point, if you are going to run it, I would dingle berry hone it and let it go. If it was in my shop, I'd try and get it straighter. Then, I'd be wetting my pants because you're getting very close to too much clearance. It's a give and take thing if you can bore it.
Just for fun, and for learning, why not torque the head on, and torque the main caps and check your bores from the underside? You may not be able to get every measurement but you should get three or four good readings.
It will help you see how far cast iron moves when it is loaded. We won't even add in temperature gradients, casting thickness variations, gasket distortion and load!! It can boggle your mind how much this stuff moves around in dynamic conditions.
Should be fun learning if you have the time. Why not give it a go?
And if you don't mind, post up your numbers. Real world stuff is educational.