Hi Todd,
I did talk to Paul at Dynamic Machine and he said that since it is still tracking the previous cut/thread, he feels like the encoder is fine it "just needs a tune up". He said to give him a call when I get it put back together and he'll walk me thru making some adjustments on the control. Not sure what he is talking about, perhaps adjusting a pot?
They did have a used pulley so hopefully I'll have it going by the end of next week.
I think I may have located an encoder if this is the correct one:
http://www.cncnew.com/listings/32844.htm