I see. Have you tried juggling the valves around, as a poor man's way of equalizing the heights? None of those valves measure the same, I assure you.
Being's your not assembled yet. Try measuring seat heights with ONE VALVE only (Int/Exh). This is your control. Now write down your heights, seat to seat, and average them. (Use a sharpie and write those numbers next to the seats)
Next, use the seat with this averaged height, and do the same with each valve. ( write down this number on each valve.) Swap accordingly. Low seat with thick valve, high seat with thin valve.
now check your spring heights and see how much improvement you have.