I'm listening to the sample with my Sennheiser HD280s. They tend to clean up the low end a little, but the bass sounds pretty good to me.
I'm not sure what you're after, but if you want to have some chiptune vibe you could maybe put some fuzz on the bass, in parallel or not.
I think using a synth as a square wave bass instead of a real bass could get you closer to that effect.
Maybe slapping a bitcrusher on it could work, but honestly I've never tried it on bass.
In Reaper there are a couple of JS plugins that could be useful to you like Waveshaping Distortion, Paranoia Mangler and Distortion (fuzz).
Anyway, this is the craziest project I've heard of in a while
.
I strongly suggest you check out these guys if you're into that stuff:
http://dopestarsinc.bandcamp.com/
http://masterbootrecord.bandcamp.com/