As much as you want this to work, its really not a good way to do it. I would remove the 002 from the setup. Once the 003 is fully functional, sell the 002 and use the money to get an 8 channel preamp with lightpipe (ADAT) connections(and WORDCLOCK would be nice). The 002 is not designed to act the way you are trying to have it do(the "stand alone" mode was designed so you could use it as a small digital mixer in a live setup). Suitable lightpipe preamps are available at all price points and here's a list that I have used:
1-Behringer ADA8200(the red one), sounds better than 002 and is a bargain
2-Behringer ADA8000(the silver one), even cheaper but not as good
3-Presonus D8- works fine, but is not worth the extra $$ to me
4-Focusrite OctoPre-also works fine, but also not worth the extra $$
5-Focusrite ISA-428/828 w/option card, really great, but way too much $$
6-Midas XL-48, Amazing on drums and the best option of price vs quality
With any of these options, you will be able to clock your system properly and avoid the headaches you now have. The 003 can slave to any of these by using the Optical(ADAT) input as the clock source, or leave the 003 as the master and send WORDCLOCK to the lightpipe preamp(and set it to use external clock). I know there are several other options that could have made the list, but none are significantly better(quality or price) unless you find a super deal
