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Are you referring to the vertical height? Assuming you are, you basically just need to measure the height protuding above the top clamp and make sure it is the same on both sides. The factory height is usually about 1/8" proud.
First, what do you mean by fork alignment? The upper sections will be aligned by the upper and lower mounts, automatically. They will only fit one way. As for the lowers, make sure you have them identified as right, or left. Look at the caliper mounts. They go on the back of the fork, so that makes the positioning possible. Mark with a "R", or "L", before removal, to simplify. You really should be consulting your factory manual before even removing the forks. If you are talking about how far up the clamp the fork should be, just enough so that the fork cap can be torqued properly without interference. Again, CONSULT YOUR MANUAL! All this information is covered quite well, with pictures. Good luck.