you can program complex time signatures and time signature changes into most DAWs and the click track and grid will adjust. but having the click track on an audio track should serve as a good enough visual guide to have things "snap" to.
"perfection is the enemy of the good"--good quote for sure and i see how it's relevant here. i've heard it most often in the context of government. but it definitely fits, and i think a "perfect" track--even technical metal--is often a boring track. not that mistakes make it better, but some amount of human variation in the timing makes the music groove. a band like Fear Factory is maybe the antithesis of that, but then again how long can you listen to Fear Factory before you get bored? Meshugga is a good example of a band that plays some crazily technical odd time stuff but always has a "groove". my advice would be only fix things that sound "wrong". i don't hear many/any of those in the soundcloud link you posted.
in any case good luck moving things along!
Thanks man. I genuinely hope this is just a funk we're in and not indicative of a larger fatal problem. It'd be really hard to walk away from the band. The guys are great and I love the music we write.