It's a shame we don't have any updates from cTrix on the SNES Sequencer (I know him and Ferris are really busy), but I ended up finding the updated version of SNESMOD on nesdev being worked on by Augustus Blackheart and, I think, KungFuFurby (not so sure on his involvement), but the clicks and pops were still there. I did find, however, an alternative solution. It takes a little bit more finagling and it does involve a little bit more work and access to a DAW and the C700 VST, but XMSNES works pretty well. It still uses Direct Gain like SNESMOD, but there's not clicking and popping. The way to set up echo/FIR is by following the instructions in the text file provided, but it leaves out some crucial info.
00-7F => 0 ~ 127 (positive values)
80-FF => -128 ~ -1 (negative values)
The XMSNES manual shows that the coefficients in instrument names spaces is essentially this:
>//7F00000000000000430
Broken down, it's:
> (read)
// = Echo Vol L/R (check C700 VST to change these values properly)
7F00000000000000 = c0 ~ c7 (FIR filter values; check above)
4 = Echo Delay (in hex)
30 = Echo Feedback (in hex)
In order to get a good gauge on how the echo with FIR filter will sound with your music, you can test out values in C700 VST and then simply copy the value (it has a button for that at the very bottom of the GUI) and paste it into your music. Set your echo to enabled using E03 and E01 for the channels you want it turned on for. The great thing is that it supports dynamic echo channel switching off or on. The new SNESMOD does as well, so that's a great thing. Two of the major things XMSNES lacks that the new SNESMOD has is Pitch Modulation and Noise Generation as well as Global Volume for your music. It will always be a value of 7F (127) even if you set the volume via Gxx in your XM module. Best way to control volume is by playing with your instrument volumes and the actual sample amplitude.
I'm personally waiting for SNESMOD to get ADSR envelopes and click/pop-less playback, but until then, I'll use XMSNES for the cleaner audio. Although, if you want better features, use the updated SNESMOD. Still highly recommended.
Note:
The XMSNES version I linked is older than the one found on Github, but it seems to be about the same in functionality, so I'm just linking the one I'm using that has great results. Also, if you're going to tweak a piece using XMSNES, be sure to delete the generated SPC before regenerating. Seems the program has an issue with replacing the file...I don't know why. I just use a BAT file to delete the SPC and then have the program recreate the SPC.