I haven't finalized where I'll put Shepard's yet. I thought about the Collector, but the horror stories about its spec kinda make me nervous. I just might try cloning them in instead, now that you mention it.
But, is it possible to do a .mod file of cloned items? I've never heard of anyone trying that. Everybody else will be replacing their Collector's Edition armors, hopefully with helmets included. Speaking of, does anybody know if Liara actually had a unique helmet in ME1 and if so, where it might be hiding in the files? I checked all the headgear files but didn't see anything especially asari shaped. I really would rather not leave her with the silly-looking breather mask if I don't have to.
I haven't seen almostfaceman's Ash armor, but I'd like to. I can't find it on the Nexus, though. 
I've got all the armor meshes extracted and working, but thanks for the offer!
Regarding the Onyx; if you want the N7 logo and stripe you'll need the HVYb model, unless you're redoing the HVYa's texture mapping, otherwise it'll be plain. I tore my hair out for a month trying to figure out why that darn stripe wasn't showing up until ELE08 pointed out that Shepard has a different model!
So far, it does look like one spec file will work for the different patterns, unless you want other bits duller/shinier or are doing different lighting. At least with my limited tests 