Hmmm…common problem but no simple answer. Around here we have a few shapers where we go for answers and help. You best bet to get this resolved is to live in Southern California or know a good prone paddleboard shaper in your town. Barring that….
What brand is the board? The fins are pretty specific. If it is a Bark you could order one from Joe and make it work with shims.
You will need to specify it is the lead fin or the tiller fin (e.g) the one that turns the board? If it is a tiller fin it is possible that you can just bend the pole a little to get it straight. Before you break ou the hammer though, remember, there really isn’t that much “play” with the fins. They need to be straight or you are going to be constantly fighting your board.
If it is a single fin, old school, mechanism with no lead/stationary fin in the front you might have a better chance in getting it resolved.
The bottom line on this is that it is always best to take it to a board shaper/builder and get a custom one built. Barring that, theoretically, it is possible buy something oversized and get the grinder out and grind away until you can make it fit and line up. That wouldn’t be our number one choice but sometimes with prone equipment you need to go a little MacGuyver.