Ok, it's a bummer.

I put a scope on the connection and it is a pulsed digital signal as suggested on the web and is does look very like baseband IR. Not being put off by that fact and after reading the FAQ, I had a look at Hijack which allows IR translation. A couple of hours later and with a small circuit to insert between the IR receiver on the front panel and the the Empeg, allowing me to invert and 'inject' my baseband signal directly into the Empeg I was ready to do some tests.
I loaded up Hijack and tried the 'button display code' but to no avail. Try as I might the Empeg just would not see the signal.

So my options look like creating my own interface to connect to the sony port using a PIC microprocessor and a digital pot or use one of the PIC circuits on the net to create unique serial data stream for each signal and then find a way to use serial commands to control the Empeg (I think that has already been done?).

Anyway after spending the past two/three hours on this I have become depressed. The fact it's nearly 1am has nothing to do with it!