Mark's comment about making the outer cowl right first is spot on.
You should consider the aftermarket inner-to-outer cowl as a pricey assembly of random sheet metal. Do not hesitate to cut it in several places, removing metal from some places and adding metal to other places until it fits the inside of the outer cowl.
Then see what you need to do to the inner-to-outer cowl to make it fit the inner cowl.
While doing all of this, I attach everything with little self-tapping hex head screws so that I can take it all apart so that I can weld the inner-to-outer cowl back together. Then you can weld the whole works into place once everything fits.
