I really don't think it's the timing. The timing should not be coming and going
like you say the idle is coming and going.

Going back to the throttle cable.....wondering if the too short cable had a bit of pull
on it and now with the proper cable, it has some slack and that might be causing
lowered idle.

Wondering if there is a locknut on one end or the other of the cable that might be
vibrating itself loose and then vibrating itself tighter.

Thinking about the cable being tight when driving, then you stop...the cable now has
less tension on it....wondering if it could be giving itself some slack and idle dropping off.