Since you are triggering SD2, using the SD2 map, as you are, is correct.
The map is for where you are going, not where you are coming from (ie. destination, not source).
If you were sending the output of the MIDI track to the TD-4, then you would map to the TD-4.
However, I don't believe a generic TD-4 map would be meaningful, as you have numerous sounds to choose from.
In Greg's example, The Acid drum kit is a specific set in the Alesis SR-16 library. The kit is predetermined by the module, and the map is pretty straightforward.
Does that make sense?
As for click/pops vs latency, are you using the Quad exclusively?
Don't send the output to your built-in sound card. Ideally, the ASIO drivers for the Quad should give you the best latency.