Moper is 100% correct of course, and I would not be concerned about intake manifold fit. Setting everything up correctly is just part of doing a performance engine build. To check piston deck clearance without CNC machining can take several mockups of the short and long block.
I will put the same piston/rod in all four corner cylinders of the block, turn the crank over and measure piston top to block deck clearance. Doing this with an old piston will tell you if the block decks are out of square ( as Moper mentioned...crooked or not parallel), and will also tell you if one deck is higher than another. I have seen a block where one deck was 0.025 taller than the other.
So get your decks the same distance from the crank centerline, bored for new pistons, then put one new piston /rod in all four corners again, measure, and then you can take the block back for final decking to fit the pistons for zero deck.
Then once the block is true, mockup the long block with just block, heads, and intake. Typically when the amount of material removed from the deck surface is known, then the amount can be determined to remove from the intake manifold side of the cylinder heads.
Always mockup and recheck everything after it comes back from the machine shop. I have caught machining errors doing final mockup checks, then its back to the machine shop again.
Takes some time,but is well worth it in my opinion.