Yep, you have to go through the adjustment process. I did exactly as you did my first time. Left the springs off and set the hood perfectly. Once I put the springs back on the back edge sat about 2" higher. It has to do with the slack on the hinges rivets and the fact that the hinges are designed not only to pull the hood down but also backwards towards the firewall as they close. Kind of a swooping action down and towards the firewall. It's a double action. The trick was to pop the hood and sit a 4x4 block of wood on top of the hood latch with the hood resting on it. Then using a ratchet strap across the back edge of the hood pull it down almost flush with the cowl. Loosen the hinge bolts to the body from inside the cab and let them float into place. Tighten them up and remove the strap and check the hood alignment then. You may need to repeat the process a few times changing how far you pull the back edge of the hood down with the strap until you find the magic spot. I think I pulled the back edge down to within about half an inch or so above being flush in height with the cowl.
