After getting your four crystals, you need to transport them in the portal. Place crystals 1 and 3 (numbered in the order that they appear), pass them, and put crystal 1 in the portal. Return with crystal 3 and switch it with crystal 2 and 4. Pass them and put them in the portal. Take crystal 1 and go back, then take crystals 1 and 3 in the portal. Another crystal will appear there. Click on crystals 1 and 3 and you are done.
First, number the shore levels in the bar on the right as 1 to 7, from top to bottom. THen, number the waves from right to left as 1 to 7. When the bar is highlighted, write down the corresponding number. Wait for all seven notes, then click the corresponding numbers on the waves.