Though I got a question how timing precise your card is. There are quite a few songs on the C64 that play samples or use oscillator feedback to produce reverb effects. For these the timing of the writes and reads is critical to produce the correct output.
Can you provide something to test on DuoSID? *.SID file that I can playback on DuoSID via three existing players? Or native *.EXE DOS program that will write to 0x280 +0x01C ports which represent all SID registers?
I can run test and show timings on logic analyzer and record produced sound.
On C64 the CPU and SID run on the same clock, how close can you get with the ISA card?
SID on DuoSID can be clocked as 0.895M, 0.985M, 1.000M, 1.023M (and many more variants), ISA bus can run faster I think. At least ~5 MHz if I'm not mistaken. And speed also depends on CPU speed of the machine.
The other thing is DuoSID contains ready/wait circuit from SSI-2001 that prolongs ISA access cycle for some time.
The SSI-2001 never was meant to resemble the C64 Soundsystem on PC.
If you want this you can build yourself a HardSID ISA.
HardSID uses totally different address method. You have to, first, write address to the board, than you have to write data to the board. So it has to take two ISA write cycles for one SID write instead of one ISA write (or read) cycle on DuoSID.