Hi Logan,
Sorry for the delay – I’m currently traveling with limited access to the forum.
It’s not uncommon to have some misalignment but this amount seems like a lot. It looks like your piece 2 might be a bit wrinkled where it’s attached to the floor, which may account for it – make sure to keep the pieces flat and tight when sealing. Can you send me an email at info at diy packraft dot com? Ideally with a picture of the bottom of your packraft showing the misalignment (the full length of piece 2 at least) and can you tell me the measurement in cm or inches of the length of the outer edge that piece 2 is being attached to?
The best way to proceed from here will be to trim the excess floor material from the outside corner where it meets the edge of piece 2 to the end of the slit.