I dunno about sanding anodized aluminum, I'd be nervous about taking off the coating. But I suppose you're just suggesting a light sanding to smooth out any bumps or grittiness and let it slide easier. Just makes me nervous.
While I agree that the stock traveller is probably one of the more frustrating design points of the Hobie 18, it was designed to be simple and cost effective, so I guess we can't complain too much. It's never really worked 100% smoothly for me, and I've usually had to help it along, but I think that was just a part of what they figured would be a part of the experience of sailing a Hobie 18. Or maybe they didn't realize it'd be as troublesome as it is. In terms of weak points in the design, I think the old mast step, original mast rotator, and the stock downhaul are up there in my list of complaints. But I guess those all have easy fixes.
I'm a little curious how you plan on combining the two travellers. When you say "one large traveller," I assume you're implying that the "narrow" width of the original traveller and narrow distance between the bearings is partly to blame for all the sticking? I tend to think it's more of the amount of/direction of force. When most of the force is in the vertical and very little in the transverse, I think it's no wonder the thing doesn't slide well. All that force is just increasing the friction between the bearings and the traveller track.