Are your tulip flaps going up? If the tulip flaps dont go up, usually because of a broken clip, the top gets stuck, you can use your hand to put the flap up and it should close but you should really replace the broken clip
On my factory top, I had to pull it down to engage the guide pins. On the replacement top I have to lift the top front to engage the pins. It sags about three inches at the front when unsupported. I mention this because not everyone will have to pull down to align the pins as you so well described in your post.Just to be clear, make sure your windows are down or doors open when you put the top up. The trunk must stay open. As Suit said, be sure the flaps behind the seats are coming up when you raise the roof. You need to push the front of the roof down slightly to get the two "pins" to enter their openings on your windshield frame. The front latch must be open as you do this. Then you engage the front latch, close the trunk and push the buttresses into their openings.