If the ply is simply inconsistent throughout, there are some other things you can do to help make it more consistent. If there are spots that are low on twist, you can run your yarn through on a wheel or spindle again fairly quickly, not adding twist on the good parts but putting twist in on the low-twist spots. And, when you wash the skein, once you've squeezed all the water out, do two things to help distribute twist:
1) put the skein around both wrists like someone was going to wind it off your wrists, but then snap your arms apart a few times to stretch the skein a bit. This doesn't actually _stretch_ the skein, but it helps the twist travel around a little bit
2) whack the squeezed-out skein on a counter top a few times, from both ends. This does also lightly felt the skein, but is another way to help get the twist to travel around the skein and even itself out.
If the skein is under-plied, the overall skein will twist "S". You can run it through on a wheel fairly quickly counter-clockwise, adding more plying twist. If the skein is over-plied, the overall skein will twist "Z". You can run it through on a wheel fairly quickly clockwise, removing some plying twist.
Why are these called "S" and "Z"? Look what happens when you put an S or a Z over them -- the middle bar of the letter goes at the same angle as the twist ...
Drawings © The Bellwether, taken from Spindling: The Basics -- used with permission.
(based on a post by me to spindlers, 3/2/2007)