Jib Halyard: Use a short piece of 1/8" line lied to the tack shackle (spec is 5' 6" on a Hobie 18 / basically the same system). Run up to the halyard wire and back down to the jib cleat (you get 2:1 purchase on the halyard wire). Use a couple of half hitches to lock. Then the halyard can be slack and untie and stow... then zip the 1/8" line up in the jib luff. Be sure the properly tension the luff while the main sail is sheeted hard enough to pull the forestay tight. Page 14 and 15 of the assembly manual:
http://static.hobiecat.com/digital_assets/21SE_Manual.pdfRudder alignment: Rudder toe-in is measured for and aft at the same vertical level, so vertical alignment of the rudders is not an issue. Get close to equal but 1/8" toe-in or more is best due to slop in rudder systems. Toe-out is not good.
Leaks: Wing sockets. You can fill with water and see if they drain into the hulls.