Seeing as this is a mock up, the first thing I would do is check your work, one technique is to carefully mark the piston at the same point top and bottom at the deck, measure at full piston rock, then add the numbers and divide by 2. Note the actual numbers by the way, I would be interested in how much piston rock you have. I have been having some conversations outside of the forum on piston rock and trapped combustion and would like to see what those pistons give you
After that, even if your numbers shrink a little, I would still strip it down and either measure the decks with a set of 12 inch calipers, or have your machinist do it.
It is VERY common for FE blocks to be not only different from side to side but also end to end. Your machinist should deck the block off crank centerline and hit any number you want
Your crank/piston/rod combo should be 10.154, an uncut FE block is 10.170. So with a fresh block, you should be .016 below. I have never seen an FE deck another 10 thou taller. However, anything is possible, but the deck measurement will tell you that
If it's a parade car or show car resto, having it exactly the same really doesn't matter much and back in the day, people didn't even think about it unless they were racing. However, there is no reason not to, especially if you intend to horse around a little
BTW, some guys will cut down to 10.150 and even 10.145 regularly, I really try not to do that unless I need to. I like a 10.160 block where I can, but sometimes you can't get there, the two I am doing now are at 10.155
Your block, if able to square up at 10.160 would be .004 below and with a .041 head gasket (Felpro 1020, not engine kit Blue 8554s) would be a pretty good.street setup, same with a 10.155 deck, at that point you are near zero deck
As far as the intake fitting, it depends. It's a function of both block and head cut. So, if the heads are stock and you cut the deck, sometimes they do OK. If the heads were cut and the block were cut, often you need to do some work on the intake as well. The more you cut, the more you need to fit.