I have been unable to resolve my endstop issue so I will probably remove them and go to the limit switches which I have already tested and found to work fine. In the meantime I decided to go ahead and test the machine without them by manually setting the home position and editing the G-code to remove the homing instructions.
Success - I managed to print a part on my second try. The first time I set the extruder position too high and it simply sprayed the filament into a big pile even though it was moving correctly in the X and Y. I still had it positioned about one millimeter too high on my second try but it created the outer shell of the part correctly. The infill did not fare so well. Since there were many quick movements and changes of direction the filament did not have time to drop into position before the hot end moved. and the holes in the part were blocked by a mass of filament caused by the suspended thread being dragged over the hole before it dropped into place. They could be drilled out however so I am counting it as a success. Very big day and I was extremely happy.
Then the Gremlins arrived. When I adjusted the height again and started the third print it stopped dead in the middle of the first layer. I found that the green LED was no longer lit on the Sanguinololu and I got a message on the workstation: "USB port has exceeded voltage limits". Now everything is dead so I believe that something has been blown on the main board. Whenever I plug in the USB I get the "Exceeded Voltage" message and nothing happens. Maybe a short? One other disturbing symptom - When I power up the 12v supply the mosfet down by the thermistor connectors becomes immediately hot enough to burn my finger, and I mean immediately, like from cool to burning in less than a second!
So I may have a trashed main board. Need to do some more troubleshooting but I am too depressed right now. At least I actually printed something so that is progress.