Unless I missed something, you don't say if all the heads are misaligned over all pallets, over just one pallet, or if it's just one head that's off.
What you need to do is: level the press. Number all your print heads. Number all your pallets (or pallet arms). Pick one pallet that's FLAT and check to see if it's level. If not, level it. Most can be leveled with washers used under the mounting screws under the pallet. Then take a FLAT screen, or a piece of plexiglass that'll almost cover the whole pallet, chuck it into the first head, and see if the head is level to the pallet by measuring the space between the bottom of the frame and the face of the pallet. If not, level that. Repeat this for all 4 print heads. Then use the plexi or frame in the LEVELED printhead and level the other 3 pallets, assuming that the pallet surface is FLAT. If not, replace the pallets and then level them.
Numbering your printheads and pallet arms will help you sort out press problems in the future. If one printhead is always going out of registration on all pallets, then you know to look to the print head for a solution. If the misregistration is only on your #3 pallet, you know to look there.