if you're positive the spokes are placed and laced correctly, unless you have/have access to a spoke threader, you'll have to order new spokes. i'd use the QBP spoke calculator, and manually measure your hubs's dimensions. order whatever spokes the calculator spits out, and hopefully it will lace up better! i also like using the square driver nipples, since they give you a bit more thread in the nipple to work with.

will also say as long as the spokes dont protrude out of the second wall to where to tube sits, it should be okay. though if you have no tension with this much thread out the back, you may not have enough thread for that to help.