Actually, this may help. Reading the manual I can see that the switch has 4 states.
PC-1(MAC), PC-2(MAC), PC-1(PC), PC-2(PC)
The PC-1 settings are 31.25K (bit/sec) and the PC-2 settings are 38.4K (bit/sec). Still, the difference between PC and MAC are unclear from the manual.
Hmmm.....MIDI Baud rate is definitely 31.25K.....but I remember reading that a PC's serial port was not a "flexible" one (unlike the Amiga's). It could only do set baud rates, of which the MIDI baud rate was not one. Therefore, PC serial port MIDI interfaces were much more complicated things that required more circuitry to translate the baud rate on the fly. So, I don't understand your switches...
Maybe this has changed with later PC's. Perhaps early PC serial ports could only do 38.4K and hence the need for the switch.
So I would definitely try it at 31.25K with the Amiga. I'm not sure it will work - while Amiga interfaces had less circuitry than PC interfaces (as the Amiga could natively do 31.25K) it still had SOME circuitry which must have done something important (between the Amiga's serial port and the MIDI instrument). Some of that might have been optical isolators.
As the SC88 has two MIDI in ports, i'd try using it as two different MIDI instruments connected to the Amiga. But that all depends on how many OUT ports your MIDI interface has. There's a few Amiga interfaces that have 2 or 3 MIDI out ports out there. Use a sequencing software such as Music-X or Dr. T's and assign two seperate channels to your two MIDI ports of the SC.
As for hooking two separate MIDI cables between the Amiga and the instrument, as some have suggested - I don't think that will work either. What would the point be? The interface would still transmit the same signal containing all 16 MIDI channels on both cables. Your instrument is merely set to "filter" each incoming channel to a separate patch/control within itself. My interface has three outputs, but they all just output the same MIDI signal. Even on an interface with only one output such as yours, you can still have different parts of a song assigned to different MIDI channels, and have, for instance, a flute playing all the channel 1 notes, and a drum playing all the channel 10 notes, etc, etc. etc.
My SC55 has two MIDI inputs on it, but one's meant for getting info from a sequencer, while the other is for a controller keyboard - so you can play live to sequenced parts (if your not already feeding the live keyboard signal through the sequencer TO the SC88).
There are MIDI interfaces (Blue Ribbon's triple play) that will output a totally discreet 16 MIDI channels on each output, but theses are very rare and only supported by a handful of software titles.
I notice that the SC88 has an option to map its voices to the SC55 layout. This might help if you ever use Bars & Pipes and the SC55 tool it has.
I really like my SC55 and would buy another one if it ever broke or got stolen. The SC88 sounds even better. I find it funny when/if people think of these as obsolete or old - they sound fantastic and if one can't make good music with them I think it's more a question of his/her creativity rather than the limits of the instrument.