What kind of assembly did IDA make for you? Did it read and integrate the symbol file from lib16534.sl? Can you assemble what IDA produced and will it run?
If you had the C source, you could do profiling. I don't know if an equivalent exists for assembler, but you might be able to call out to the C library and have monitor() to set it up.
Another thing to do is to probe the ADC to confirm it's being read out at a high speed. I doubt the card or backplane is constraining the data readout, but it wouldn't hurt to confirm this before digging into the software side. You'd have to figure out which ADC pins were the data bus and bus clock.
Without the original source code, I think it's going be be difficult to figure out what's slowing it down. I don't think it's worth the effort, but if you want to pursue it, I'll add where I can.