I just ordered the keycap puller from elitekeyboards. I was planning on rearranging the qwerty layout to dvorak- leaving all the non-letter keys in their spots. The letters will be interchangeable, right?
Sorry, no. The Filco boards (like most keyboards) use differently-shaped keycaps in each row.
This picture shows a set of blank Filco key caps in their normal order on a flat surface. The picture doesn't highlight it well, but if you look closely you can see the shape differences:

Look especially at the number key row vs. the Z-row, if you're having trouble seeing it.
You can swap the keys around within the rows without problems, but if you swap between different rows, the tops of the keys will be at different heights and angles.
Try swapping a few keys from different rows to see what you think. The mismatched feel would annoy me a lot, but you may not mind as much.
Even if you don't end up swapping your caps, the puller will still be useful for situations like when you want to clean the key caps.