Hey Nicholas,
If you can somehow make sure you use the alg 2 or 4 times (or a multiple), then there would be a way out.
If you just use it once, it would be 90 degrees misaligned. If you use it twice, it would be 180 degrees off, which there is a parity alg to fix. Check this page
http://wiki.superliminal.com/wiki/3%5E4 for the alg.
If you could use it 4 times, then it'll just align itself again.
Unfortunately, I'm not sure if it's possible to fix just a 90 degree alignment.
Earlier on we had another guy who was doing a 4x4x4x4 and there was a similar issue. They had to use an alg that gave them a 90 degree misalignment on one of the inner layers. Unfortunately, if I remember correctly, they had to redo their solve and hopefully avoid the situation.
Alvin