Yeah that is a little tricky.
Part 1
In part 1, you need to place all the alphabets such that the gaps between them match the blocks in the clue sets. All placements can be logically deduced. For example, B and I must be in the 4th and 5th column next to each other and must have at least 3 rows above. Since X/Y is already in the last row, B and I must go in the 4th row.Part 2
In part 2, you have to pay close attention to how each shape moves and interacts with each other. For example, the squares move clockwise along the border. You'll also need to figure out which shape gets priority when multiple shapes are trying to occupy the same box.Part 3
You'll need to use both Part 1 and Part 2 for this.First part of Part 2 shows that the order of precedence when finding the coordinates for the letters is triangle > circle > square. Also see how Doctor Trout got the first two letters.
If you still need help with the solution, you can download CrypticSolutionImagesV2.4 from the downloads section above. :)