We saw that Cap had all the pieces of the shield, after Beyonder-empowered Doom had shattered it. Cap didn't need to understand the molecular structure to reassemble it because the planet did that for him (Just as it allowed Ben Grimm to assume a human form without him understanding genetic engineering). He simply had to imagine it whole with enough willpower and it would become so. In Secret Wars he achieved it because he HAD the willpower to make it so, the Waid story would seem to imply he couldn't remember the shape and "feel" of the shield he'd been carrying with him for 40 years.