Wow ...5 pages and 47 replies to figure out it was the master cylinder...which was diagnosed in the first reply to the thread...
If you ever suspect the MC...crack the bleeder open...not rocket surgery...
Tom we had rebuilt the master and caliper and that was mentioned right in the beginning , we thought the rebuild would have sorted the issue but it didn稚 , so we replaced it
Skinman ... all was rebuilt from the start of the thread , rebuild wasn稚 enough .
Don't take this the wrong way, but in my aviation career I heard that so many times it became a red flag that something was done wrong. In your case, your brake system wasn't properly or completely rebuilt or you wouldn't have continued to have problems. No fault, it just is how Murphy works. Instead of chasing my tail like you did, I would have pulled the entire system apart and rebuilt it again. If it still had a problem, I would have replaced the master and caliper with rebuilt used parts and rode off into the sunset. It takes less time (which is hard cash $$ in the real world) and aggravation than trying to find out what is wrong while assuming that everything that was done was correct and working.
You found the problem and are back on the road. That's all that matters in the long run. Ride safe.