Strobe will resolve the white balance problems to a large degree, because the strobe is a light source that is very close to the subject, so the light you are using for you shot has only travelled through a few metres of water, so only a small amount of the reds end of the visible spectrum will have been absorbed. Ambient light (i.e. from the sun) will have travelled through the entire water column above you, which is why the ambient light has had the red end of the spectrum largely absorbed.
Thus when you are using the strobe, the colour temperature of the light is pretty consistent. You will probably find that one of the pre-set white balances will look quite natural when using the strobe, or if not, you will be able to use a previously shot (with strobe) underwater picture to set the custom white balance.
Surely the 400D came with software that allows you to process the raw files? I thought only Nikon made you pay for the software to do it! I appreciate that the workflow is a bit of a drag, in that you can’t do it all in Photoshop, however, it would appear that the alternative is to upgrade you Photoshop CS3 so you can use the Camera Raw v4.2 plugin, which supports the new EOS40D, so I assume it supports the 400D.
Hopefully that makes sense!
Graham