Suntour a-3000 6-sp shifters with 5-sp freewheel?
 

I am replacing the shift cables on a 1995 Trek 800 "Antelope", and noticed that the thumb shifters are 6-speed indexed (Suntour alpha-3000 Accushift) but the freewheel is 5-speed. I started by setting the cable in the high-gear position on the shifter, relying on the low-gear set screw to limit the shifter from going into the sixth position. However, the limit screw is "mushy" in this regard - the screw contacts a plate that is attached to the anchor bolt - this is a movable part that seems to affect alignment but doesn't provide a firm stop. Thus, pushing the thumb shifter past the fifth position would move the RD a few millimeters toward the spokes, enough to cause some contact between the spokes and the cage. I changed the approach to set up the high gear in the second shift position. This works out better in low gear, and there doesn't seem to be any harm in having a useless shift position in the high gear side.

Is the second approach okay, or am I missing something?

For reference, here is a pic. The surface that the low-gear limit screw (on the left) contacts is attached to the outer section of the RD.

http://i1156.photobucket.com/albums/...07-00280-1.jpg

I like your second approach, it's the one I use. That way, the "extra" shift position loosens an already slack cable rather than jamming against a limit stop. The same concept works for using a triple front shifter on a double crankset.

I haven't come across a limit screw that operated mushy.
I can feel cable stretch, but the derailer doesn't move past that point.

What happens if the limit screw is turned in further?
If the shifter then fails to hold low gear, I believe the shifter is worn out.

This often happens with older shifters, particularly certain Suntour shifters, that suffer what in effect is a worn detent.

I think this results from a taut cable cyclicly pulling on the shifter in response to frame flex, thus causing slight but continuous movement against the detents in the shifter. If the limit screw was over-tight for a long time then the lowest-gear detent probably got worn out this way.

This also happens to Shimano downtube shifters on occasion.

Form derailers I've seen, the limit screws inhibit the operation of the parallelogram - the screw is anchored on one part, and runs against a different part so that the angle cannot exceed a certain amount one way (high) or the other (low). (I know I'm probably not describing it correctly). This derailer has the low limit screw anchored on the outer part of the body, and sets against a part of the cable anchor that is also anchored to the outer part of the derailer body. The low-limit screw is always touching the surface, even in high gear. If I adjust the screw, the cage will move in or out, but that adjustment doesn't seem to be related to the inner limit of travel. So even though the screw is up against the "stop", I can push the derailer inwards a little bit. This doesn't seem to involve the shifters, they are working properly since I last adjusted the setup, and there is no issue with centering or holding a gear. This derailer was just different than what I've seen before, and I want to make sure there isn't a different technique to handling low-gear limit.

Now you've got me wondering if the lo-limit screw is long enough, and assuming it really is the lo limit screw, which you probably had no difficulty distinguishing.

The part that the screw touches must be spring-loaded against the screw, and moves with the screw, with some part of it contacting a hidden stop point at the travel limit.

Tried a longer screw?

I think I'm going to leave it as-is for now, it's working fine and I worry about over-thinking the problem :)