You are confused on a few things here(but its not a big deal). You don't bypass the 003 converters(they still convert eh 003 inputs to digital, and the 003 outputs back to analog). You substitute the 003 clock for the ISA clock(any time you connect things via digital, you must designate one master clock). I used to have pretty much the same setup, but I didn't have the 11R, which may require some futzing, depending on if you use it via analog or via digital.
Connecting the 428 and 003 is done with just a single lightpipe "cable", but there are several ways to clock the system. Set clock source(in Pro Tools) to Optical and the ISA will act as the master(make sure the sample rate on the ISA matches the sample rate of your session!!!).
Alternately, connect a wordclock cable from the ISA wordclock output to the 003 wordclock input and then select(in Pro Tools) Wordclock as the clock source. 3rd option, connect a wordclock cable from 003 out to ISA in and leave the clock source set to internal(so the ISA slaves from the 003). You might try all of these options to see if you can hear if one scenario sounds better(my own 2 cents, it sounded fine either way).
As for the 11R, if you connect it via analog, everything above should be fine. If you need to connect via digital, it gets a whole lot more complicated because it only has SPDIF connections and no wordclock. Here is how I would TRY it:
SPDIF cables connecting 11R out to 003 in and 003 out to 11R in. Set the 11R to sync to SPDIF and send 003 wordclock to the ISA. The ISA would be set to external clock and Pro Tools would be set to internal clock(the 003 is the master).
I can't think of any way to use the ISA as the master with the 11R connected via SPDIF
Re the extra inputs on the ISA(5 thru 8), these can be used to connect most any external mic preamps that have a line-level output(I used mine for 4 preamps in an API lunchbox)
