Twist removal

[Busted Knuckles]

I have removed the decks from the boat , and now notice a twist to the stbd side . The stbd is about an inch or less than the port rail . I thought that if i evened it out while installing the new deck that it would straighten out . Doing this worked somewhat but there is still a 1/8 to 1/4 difference port to stbd . I have removed all of the decks on the coveringboards and was going to raise the twist out of it as I install new coveringboards, hoping that this will work . any ideas , am I doing this right?